association	dataset	threshold value	standardized value
TCF12_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2A_MCF-7_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3973_KD_CDK4/FYN_SRP190631	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
estradiol_homo sapiens_gpl570_gse23610	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
GSE139016_0_v_1_disulfiram_human	RummaGEO Drug Perturbation Signatures	-1.0	null
FOXA1_T47D_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
lymphnode_4b	HPA Tissue Sample Gene Expression Profiles	1.0	1.21027
hsa-miR-670	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
CTCF_bronchial epithelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MXI1_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
mRNA_JARID2_20075857	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
Protein phosphatase type 1 complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.518
motor nucleus of trigeminal nerve	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.888681
496100543_FWM_probable Alzheimer's disease_TBI_78_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.62253
Perturb_7384_KO|KD_SMG7_ERP122822	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
POLR2AphosphoS5_G1E-ER4_mm9_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Liver disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.616
GTEX-XQ3S-2726-SM-4BOP2	GTEx Tissue Sample Gene Expression Profiles	1.0	0.92838
Perturb_401_KD_RNF113A_SRP201913	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.20449
MAX_HCT116_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE71385_1_v_0_cdk8_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-FR-A7UA-06A-32R-A352-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Urinary system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.562
GSE155162,GSE155169_1_v_0_buparlisib_human	RummaGEO Drug Perturbation Signatures	1.0	null
EZH2_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9976_KD_G3BP2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.82537
pb1	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.899
Liver hepatocellular carcinoma_LIHC_TCGA-CC-5263-01A-01R-A131-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CUX1-19635798-MULTIPLE HUMAN CANCER CELL TYPES-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
MYC_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8214_KD_SRSF5_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.4868
hsa-miR-340	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
CTCF_choroid plexus epithelial cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15146_KD_CUX1_SRP343012	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.16732
A-Vietnam-1203_CIP048_RG4-2004(H5N1)NS1trunc_7Hour_None_GSE43204	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.53511
USF2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-BP-5196-01A-01R-1426-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PPP2CB	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.04916
Perturb_634_KO_HOXD3_ERP117895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.30121
p107_Deficiency_GDS3176_606_mouse_Skin	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
REST_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
amygdaloid complex_13 pcw_F_12834	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.02799
t60-adrenal_consensus	MoTrPAC Rat Endurance Exercise Training	1.0	2.50449
GSE120612_4_v_5_etoposide_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_7708_KD_Spt6_SRP132004	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.08947
GSE86507,GSE86509_3_v_2_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
MET_knockout_248_GDS3148	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	1.0	2.20569
GSE157960_0_v_3_progesterone_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Orbital area, medial part, layer 5	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07914
Perturb_11388_KD_BRG1_SRP261084	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.65357
GSE206516,GSE206518_2_v_7_ptdss2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE198165,GSE198166_0_v_1_zfp266_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_8233_KD_RBM15_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.69921
Prostate adenocarcinoma_PRAD_TCGA-YJ-A8SW-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
OB olfactory fiber layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.82604
organelle	GO Cellular Component Annotations 2015	1.0	null
MCF12A	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	0.642782
Calu-3	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-1.98133
Perturb_9973_KD_CSTF2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.91157
Perturb_17247_KD_Brd2_SRP201499	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	4.56076
Lung adenocarcinoma_LUAD_TCGA-44-7667-01A-31R-2066-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_skeletal muscle cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
H3K9me3_Adult Liver	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_11919_KD_PDPN_SRP071702	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.15172
GSE160765_2_v_1_twist1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
reticular nucleus of thalamus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.64559
layer 6a of PrS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.34629
caudal ganglionic eminence_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	2.51651
CHD7_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
intrinsic component of membrane	GO Cellular Component Annotations 2015	1.0	null
Perturb_10047_KD_GEMIN5_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.41611
GSE74490_0_v_1_triptolide_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_6127_KO_NEUROD1_SRP170936	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.02742
GSE242199_9_v_11_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
RARA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	59.601
CTCF_small intestine_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MXI1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
intermediate stratum of CoPV	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.11187
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44043
Perturb_12338_KD_TFEB_SRP226507	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.3113
Perturb_10056_KD_SUPV3L1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.32021
GTEX-XMD1-0011-R1A-SM-4AT4C	GTEx Tissue Sample Gene Expression Profiles	1.0	1.99066
dexamethasone_rattus norvegicus_gpl1355_gse29912	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
TAP2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.09556
GSE231720,GSE231724_2_v_1_setd2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
ISGF3 complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.798
Uterine disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.471
Perturb_10251_KO_WT1_ERP126063	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	15.4099
H3K4me2_myocyte_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
STAT3	ENCODE Transcription Factor Targets	1.0	null
MOLT-4	COSMIC Cell Line Gene Mutation Profiles	1.0	null
PMC12021535-CPH4-15-e70011-s001.xlsx-S21-KLF2_KLF2	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_12726_KO_MITF_SRP255094	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	13.8741
POLR2A_HEK293_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-66-2758-01A-02R-0851-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2355_KD_HOXA11_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_8189_KD_HNRNPF_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.21103
Perturb_2426_KD_CNBP_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.06441
Stomach	GTEx Tissue Gene Expression Profiles 2023	-1.0	-0.550022
GSE223008_5_v_3_calhm6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CHD7_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_10431_KD_circFAT1_SRP261305	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.9791
GTEX-QDT8-0011-R4A-SM-32PKM	GTEx Tissue Sample Gene Expression Profiles	1.0	1.34732
H3K56ac_IMR90	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Pheochromocytoma and Paraganglioma_PCPG_TCGA-W2-A7HH-01A-11R-A35L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2731_KD_MBNL1_SRP258724	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	11.6667
Perturb_4764_KO_DLG2_SRP315088	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.82496
GTEX-XLM4-0011-R8A-SM-4AT44	GTEx Tissue Sample Gene Expression Profiles	1.0	2.82281
NCI-H28	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
GSE135352_6_v_4_napabucasin_human	RummaGEO Drug Perturbation Signatures	1.0	null
cisplatin_homo sapiens_gpl570_gse23553	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
Perturb_9137_KD_HMGB2_SRP106038	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.2628
H3K4me3_G1E_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
GSE188870,GSE188871_1_v_5_kat7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE57871_1_v_10_vorinostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
lateral ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.25466
GTEX-XMD1-0011-R10A-SM-4AT4A	GTEx Tissue Sample Gene Expression Profiles	1.0	1.80845
GSE193258,GSE193259_9_v_3_osimertinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
BRCA1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Esophageal epithelial cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.672
Perturb_8196_KD_TIAL1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
ETS1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Weight Loss	CTD Gene-Disease Associations	1.0	1.26083
Acute Myeloid Leukemia_LAML_TCGA-AB-2913-03A-01T-0734-13	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_6080_KD_THRAP3_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE157777_2_v_0_foxa3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H3K9me3_astrocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7620_OE_OspC3_SRP368098	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.25213
Perturb_12937_KO_SPI1_SRP342114	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.43668
Perturb_11175_KD_ZNF529_SRP201912	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.41824
NFIC_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXM1_ECC-1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZKSCAN1	ENCODE Transcription Factor Targets	1.0	null
Triple Negative Breast Neoplasms	DisGeNET Gene-Disease Associations	1.0	null
Perturb_1327_KD_COX2_SRP074235	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.77316
Perturb_2427_KD_CTBP1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.28985
preoptic region, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.824483
GSE146982_4_v_1_metformin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
LB-100_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0227982
periventricular stratum of r5Co	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07701
EFE184	DepMap CRISPR Gene Dependency	1.0	2.10698
TRIM28_U2OS_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_13662_KD_E2F1_SRP225180	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.99932
GSE109530,GSE109531_1_v_0_hdac3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE198165,GSE198166_5_v_10_zfp266_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
r5 part of dorsal cochlear nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07701
ventricular (matrix) zone of cerebellum	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.889902
H3K4me3_fibroblast of mammary gland_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
TAF1_GM12891_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
inferior colliculus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.37952
Kidney renal papillary cell carcinoma_KIRP_TCGA-B3-4104-01A-02R-1351-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K9ac_ES-E14_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE86507,GSE86509_3_v_10_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
E2F6_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE85880,GSE85881_0_v_1_tretinoin_human	RummaGEO Drug Perturbation Signatures	1.0	null
SOX9	ChEA Transcription Factor Targets	1.0	null
MAX_HepG2_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
RUNX2-24655370-MC3T3E1-MOUSE-BONE	ChEA Transcription Factor Targets 2022	1.0	null
GSE158458_2_v_3_sorafenib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-T6MN-2626-SM-32PMQ	GTEx Tissue Sample Gene Expression Profiles	1.0	1.19801
Perturb_11717_KD_MBD2_SRP194625	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.66375
GSE215086_5_v_7_batf_human	RummaGEO Gene Perturbation Signatures	-1.0	null
2893_TAFA2_P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.639719
ZNF8	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.7048
GSE151494_1_v_4_nrp1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC3906982-1471-2164-14-830-S1.xlsx-Sheet1-Table_S1_HOXC9-responsive_genes_HOXC9	Rummagene Transcription Factor Associations 2026	1.0	null
GTEX-S7SE-0011-R2A-SM-2XCDC	GTEx Tissue Sample Gene Expression Profiles	1.0	1.3426
Perturb_17649_KD_AFF1_SRP334520	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.36681
FOXD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	218.464
Perturb_18482_KD_DNMT1_SRP261597	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.6737
SUPB15	CCLE Cell Line Gene CNV Profiles	-1.0	-2.50515
H3K4me3_ES-Bruce4_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
18338247-SuppTable4A	GeneSigDB Published Gene Signatures	1.0	null
ion binding	GO Molecular Function Annotations 2015	1.0	null
CTCF_bronchial epithelial cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Anterior cingulate area, dorsal part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.42713
CTCF_MCF-7_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE218060_7_v_0_decitabine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Primary somatosensory area, lower limb, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.02037
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-C5-A2LS-01A-22R-A22U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC12499388-ADVS-12-e01774-s002.xlsx-Table_S1-Table_S1_Differentially_Expressed_Genes_between_wild-type_and_TET3-knockout_PANC-1_cells_TET3	Rummagene Transcription Factor Associations 2026	1.0	null
PMC9469581__F5	PFOCR Pathway Figure Associations 2024	1.0	null
GSE126345_4_v_5_hcrt_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H3K4me1_Breast Myoepithelial Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
RPS10	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.55251
Anterior olfactory nucleus, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.4186
GSE203308_14_v_0_brf1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Peripheral nervous system neoplasm	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.289
GSE233647_2_v_3_docetaxel_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC4021073-1471-2407-14-278-S4.xlsx-Sheet1-Supplementary_Table_S5_Genes_with_GATA3_ChIP-seq_peak_within_10kb_from_transcription_start_site_TSS_GATA3	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_8289_KD_NONO_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.06632
COX8A	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.13055
GTEX-QDT8-0011-R10A-SM-32PKG	GTEx Tissue Sample Gene Expression Profiles	1.0	0.886272
3369_GINS1_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.748629
Lung squamous cell carcinoma_LUSC_TCGA-70-6723-01A-11R-1820-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_12951_KD_ALKBH5_SRP247667	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
MAZ	ENCODE Transcription Factor Targets	1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_10 mos_M_12977	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.12113
Perturb_8112_KD_SUPT6H_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.95889
GSE174498,GSE174500_3_v_4_asparaginase_human	RummaGEO Drug Perturbation Signatures	-1.0	null
SG in temporal polar cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.940066
EZH2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE108675_3_v_0_slc1a4_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE146074_6_v_7_ly6e_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Obesity_Adipose tissue_GSE4692	GEO Signatures of Differentially Expressed Genes for Diseases	-1.0	-3.0424
RAMOS	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.987652
Perturb_12241_KO_ZMYND8_SRP343066	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.65799
H3K4me3_B cell_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
REST_neural cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NIH:OVCAR-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.11355
H3K27ac_H1 BMP4 Derived Mesendoderm Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Sodium Salicylate_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0288187
H3K4me2_astrocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_Panc1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3013_KO_TLE4_SRP298305	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.62733
GSE235701,GSE261434_2_v_3_enasidenib_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me3_C2C12_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Harderian gland	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.652
CBX3_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSK1059615_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.01995
PMC11131031-pwad060_suppl_supplementary_tables_s3.xlsx-FOXO1-knockout_bulk_RNA-seq-Differentially_expressed_genes_identified_in_bulk_RNA-seq_of_FOXO1-_-_vs_FOXO1_hMSCs_FOXO1	Rummagene Transcription Factor Associations 2026	1.0	null
RBBP5	ENCODE Transcription Factor Targets	1.0	null
Nucleus accumbens	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.12093
H3K4me3_WI38_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7489_KD_SIN3A_SRP173465	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.7332
Hematologic cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.493
Perturb_2455_KD_ZNF213_SRP243455	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K4me3_keratinocyte_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
mediodorsal nucleus of thalamus_16 pcw_M_12837	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.02823
Perturb_449_KO_RPA_SRP158719	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
POLR2AphosphoS5_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-BA-4077-01B-01R-1436-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
496100455_FWM_dementia_TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.22547
PMC4392212-gutjnl-2013-306620-s9.pdf-4-SMAD4_SMAD4	Rummagene Transcription Factor Associations 2026	1.0	null
GSE205540_2_v_3_phloridzin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
RFX5	ENCODE Transcription Factor Targets	1.0	null
cerebellar cortex_8 yrs_M_12841	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.855028
PMC6151027-12864_2018_5080_MOESM3_ESM.xlsx-E20_vs_D1_815_AR-DEGs-Symbol_AR	Rummagene Transcription Factor Associations 2026	1.0	null
OVCAR8	CCLE Cell Line Gene Expression Profiles	1.0	1.70347
Perturb_7950_KO_BAZ1A_SRP100570	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.12206
GSE211989_0_v_1_nlrc3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_CD14-positive monocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_G1E_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Gall bladder cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.958
Pancreatic Neoplasms	CTD Gene-Disease Associations	1.0	1.05648
Perturb_14389_KD_PAX8_SRP276625	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
r2 part of basointermediate reticular formation	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.26269
posterior (caudal) superior temporal cortex (area 22c)_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.04734
TRIM21	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.79679
GTEX-N7MT-0011-R2a-SM-2I3GI	GTEx Tissue Sample Gene Expression Profiles	1.0	1.45567
Perturb_8224_KD_DDX19B_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.08707
absent amnion	MGI Mouse Phenotype Associations 2023	1.0	null
CTCF_fibroblast of lung_hg19_6	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF384	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	232.938
amygdaloid complex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.951106
GSE181966_0_v_3_has2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
15843827-TableS6	GeneSigDB Published Gene Signatures	1.0	null
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.25969
Perturb_9966_KD_SF3A3_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.91466
GSE191015_0_v_3_gsdmb_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE235701,GSE261434_0_v_3_enasidenib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Gastrointestinal system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.968
EFM-19	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.03096
PMC10794847-mmc5.xlsx-PIAS1_KD_down-Table_S4_Differentially_expressed_genes_with_PIAS1_knockdown_in_the_progenitors_state_Related_to_Figure_5_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Mucosa	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
496100411_FWM_no dementia_no TBI_78_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.13808
SARS-CoV_0Hour_23935999_GSE47961	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.94961
H3K27ac_skeletal muscle myoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Sensory system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.097
posterior (caudal) superior temporal cortex (area 22c)_26 pcw_F_12949	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.90248
H3K4me3_BE2C_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_cardiac mesoderm_hg19_8	ENCODE Histone Modification Site Profiles	1.0	null
EZH2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Acute Myeloid Leukemia_LAML_TCGA-AB-2853-03A-01T-0734-13	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_11761_KO_Arg2_SRP198795	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	2.13037
GTEX-QMR6-0011-R6A-SM-32PKP	GTEx Tissue Sample Gene Expression Profiles	1.0	1.07071
Carcinogenesis	DisGeNET Gene-Phenotype Associations	1.0	null
DPY-21335234-ESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
H3K4me3_cardiac fibroblast_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
GSE256181_2_v_3_etv2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
NCIH2342	CCLE Cell Line Gene CNV Profiles	1.0	1.35116
GSE202434,GSE202438_15_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE224096_3_v_0_cocaine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE226249_2_v_3_pirfenidone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
paracentral lobule, posterior part, right, bank of cingulate sulcus	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-2.52698
Lung squamous cell carcinoma_LUSC_TCGA-58-A46M-01A-11R-A24H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
NEUROG1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.52
GABPA_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Alzheimer's disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.039
CTCF_skin fibroblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
OCI-M1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.73303
Liver hepatocellular carcinoma_LIHC_TCGA-CC-A8HS-01A-11R-A36F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GTEX-T6MN-0011-R2A-SM-32QOW	GTEx Tissue Sample Gene Expression Profiles	1.0	1.49447
Perturb_12107_KD_CCND1_SRP244245	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.7858
GSE179974_3_v_1_carboplatin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE77108_3_v_9_saha_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE151090_5_v_3_verteporfin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_12934_KD_DHODH_SRP340404	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.31626
GSE160817_0_v_8_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
caudal ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.59024
Perturb_8144_KD_PABPC4_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.4498
Male reproductive system disease	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
PMC7346435-12864_2020_6860_MOESM6_ESM.xlsx-H1_ZF_Oocyte_Specific-Gene_SymbolH_CREBZF	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me3_testis_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_6483_OE_ASCL1_SRP292702	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.62251
Perturb_2774_KD_TRIM25_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE154767_1_v_5_adam10_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_3622_KO_SMARCC2_SRP127343	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.51618
Perturb_9988_KD_CNOT7_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.58337
Glioblastoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.445
7477_RPL7A_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.893251
Perturb_9785_KD_EPS15_SRP339484	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.67241
Perturb_3262_KO_VHL_SRP337931	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.7658
TAF1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
KYSE270	CCLE Cell Line Gene CNV Profiles	1.0	2.52272
PMC9753996-jci-132-160767-s182.xlsx-IRF4_assciated-ABCA7_IRF4	Rummagene Transcription Factor Associations 2026	1.0	null
tamoxifen_homo sapiens_gpl570_gds4095	GEO Signatures of Differentially Expressed Genes for Small Molecules	-1.0	null
MDA-MB-435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.911896
Perturb_9669_KO_NR1H4_SRP115904	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.83225
H3K4me3_cardiac mesoderm_hg19_6	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me2_myotube_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_GM12891_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MYCN-28898695-NB1643-HUMAN-NERVE-NEUROBLASTOMA	ChEA Transcription Factor Targets 2022	1.0	null
GSE166004_7_v_0_pld1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC12254391-41598_2025_8960_MOESM5_ESM.xlsx-fig-Supplemental_Table_6_Differentially_Expressed_Genes_DEG_between_siRNA_DLX4_and_siRNA_control_n_3_RA_FLS_cell_lines_per_treatment_group_DLX4	Rummagene Transcription Factor Associations 2026	1.0	null
Posterolateral visual area, layer 6b	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.6392
H3K4me1_megakaryocyte_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE126127_2_v_3_prmt1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_12653_KD_KPC1_SRP071659	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.34931
H3K4me3_epithelial cell of esophagus_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_IMR-90_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TAF2-19829295-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Squamous Cell Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
GSE158632_3_v_5_oxyquinoline_human	RummaGEO Drug Perturbation Signatures	-1.0	null
SP4_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Uterine Carcinosarcoma_UCS_TCGA-N7-A4Y0-01A-12R-A28V-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Anterior olfactory nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.02682
membrane	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
Prostate adenocarcinoma_PRAD_TCGA-EJ-5507-01A-01R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE200352_11_v_3_pparg_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_9637_KO_CHCHD2_SRP212876	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.00584
GSE134191_3_v_1_metformin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Brain disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.306
GTEX-X4XX-0011-R5A-SM-46MWN	GTEx Tissue Sample Gene Expression Profiles	1.0	1.71425
Perturb_7662_KD_CTCF_SRP072272	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.61135
721_B_lymphoblasts	BioGPS Human Cell Type and Tissue Gene Expression Profiles	1.0	1.16758
Perturb_8973_KD_RBL1_SRP218370	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
VI, left, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.44238
central medullary reticular group, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.19562
skeletalmuscle_b	HPA Tissue Sample Gene Expression Profiles	-1.0	-2.07549
Perturb_9249_KO_Setdb1_SRP332486	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	8.48888
Perturb_6763_KO|KD_SERPINE2_SRP103746	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.7783
GSE87412,GSE92423_0_v_4_dnmt3a_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
RELA	ENCODE Transcription Factor Targets	1.0	null
GTEX-T5JC-0011-R7A-SM-32PME	GTEx Tissue Sample Gene Expression Profiles	1.0	0.907265
regulation of canonical NF-kappaB signal transduction	GO Biological Process Annotations 2025	1.0	null
MYC-19030024-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
E2F6_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Thymic Carcinoma_Thymus_GSE2501	GEO Signatures of Differentially Expressed Genes for Diseases	-1.0	-2.05909
NCIH3255	CCLE Cell Line Gene CNV Profiles	1.0	1.38221
GSE153836_11_v_9_fluoxetine_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-N7MT-0011-R5a-SM-2I3G6	GTEx Tissue Sample Gene Expression Profiles	1.0	0.973578
H3K4me2_K562_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
EP300_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
YY1	ENCODE Transcription Factor Targets	1.0	null
NCI-H1650	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.12144
Rectum adenocarcinoma_READ_TCGA-EI-6917-01A-11R-1928-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
FOXA1-25552417-VCAP-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
failure to gastrulate	MGI Mouse Phenotype Associations 2023	1.0	null
SCLC-22H	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42522
Perturb_8929_KD_CHD4/ARID1A_SRP350011	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.902
Perturb_2066_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.53265
eGFP-HDAC8_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE89018_12_v_14_cry2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE130383_1_v_3_gps2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_14443_KO_Mtor_SRP106322	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-10.5565
GSE167886_2_v_0_chd7_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
JUN_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
496100608_FWM_no dementia_no TBI_78_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.11809
VZ in caudal hippocampal proper	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.44093
substantia nigra, pars reticulata, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.979679
PMC7893038-41598_2021_83450_MOESM3_ESM.xlsx-DBP_Traj_AMR-GENE_DBP	Rummagene Transcription Factor Associations 2026	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-DK-A1AE-01A-11R-A13Y-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_GM12875_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal papillary cell carcinoma_KIRP_TCGA-BQ-5894-01A-11R-1592-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Anteromedial visual area, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.42848
GSE195568_2_v_7_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K27ac_ES-E14_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
TEAD4-22529382-TROPHECTODERM-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
parietal neocortex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.29937
RAVER2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.01995
SOX8	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.0154
Perturb_2598_KD_PRMT6_SRP131294	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.65099
GSE240386,GSE242143_8_v_6_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
KYSE-180	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
POLR2A_GM12891_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.68694
18231642-TableW1	GeneSigDB Published Gene Signatures	1.0	null
MDAMB436	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	-1.0	-0.872847
KDM5B-21448134-MESC-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
Perturb_9904_KD_SND1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.46885
GSE145215_0_v_1_krt13_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
10663_ZNF830_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.596104
GSE186440,GSE186443_3_v_5_daxx_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_9406_KD_GATA6AS_SRP279802	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.34853
Ovarian disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.541
CTCF_GM12869_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
bmi1_17452456_medulloblastoma_lof_human_gpl570_gds2724	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.311368
H3K27ac_brain_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-Q2AG-2826-SM-2HMJQ	GTEx Tissue Sample Gene Expression Profiles	1.0	0.824181
H3K4me3_K562_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
FOXA1-33576154-HUMAN-LUNG-PROSTATECANCER	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_2303_KD_BRCA2_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.35794
GSE142210_9_v_10_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_1081_KO_BACH1_SRP174544	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.35954
MAX_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8091_KD_NOL12_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.46499
hsa-miR-4765	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.55165
Kidney renal clear cell carcinoma_KIRC_TCGA-B8-4146-01B-11R-1672-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
intermediate stratum of THyB-I	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.26711
GTEX-TSE9-0011-R9A-SM-3DB7Q	GTEx Tissue Sample Gene Expression Profiles	1.0	0.875756
bonemarrow_6c	HPA Tissue Sample Gene Expression Profiles	1.0	1.01609
MEF2A_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15502_KD_GUCY1A1_SRP148609	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.29053
GSE142210_11_v_7_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
PCI4B	DepMap CRISPR Gene Dependency	1.0	4.46603
CNOT3-19339689-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
Nervous system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.655
MAZ_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15486_KD_SIM2_SRP218853	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.79397
377_AP2M1_P1	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.721024
Lung adenocarcinoma_LUAD_TCGA-35-4123-01A-01R-1107-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_mammary epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE190947_2_v_0_xbp1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_2069_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.43161
HGC27	CCLE Cell Line Gene CNV Profiles	-1.0	-1.56548
ZNF143_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC5691083-41467_2017_859_MOESM6_ESM.xlsx-FDR_0_1_RELB_RNAi-Unnamed_1_RELB	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me3_CD8 Naive Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_4376_KD_CREBBP_SRP072506	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.89496
ChIP_MYCN_18555785	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
Perturb_17651_KD_HEXIM1_SRP334520	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.5774
Fetal Growth Retardation	CTD Gene-Disease Associations	1.0	1.05423
POLR2AphosphoS5_U-87 MG_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
red nucleus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.27927
globus pallidus, external segment, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.53964
H3K9ac_MEL cell line_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
EB1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.930203
hsa-miR-328	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.07142
Fibrosarcoma	DisGeNET Gene-Disease Associations	1.0	null
Perturb_16316_KD_POU2AF1_SRP336261	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.8716
Kidney disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.21
NCI-H1435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02908
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.74088
GSE88819_6_v_10_tug1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Sarcoma_SARC_TCGA-KD-A5QT-01A-11R-A27Q-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Organ system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	2.097
ELF1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE206516,GSE206518_6_v_7_ptdss2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE133691_1_v_3_lgr5_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Paclitaxel_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0208101
GSE129858,GSE129859_1_v_3_robo1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
POLR2AphosphoS5_G1E_mm9_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE211963_0_v_3_cd200_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-CH-5752-01A-11R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE186440,GSE186443_4_v_5_daxx_human	RummaGEO Gene Perturbation Signatures	-1.0	null
NAMALWA	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.21724
ventromedial hypothalamic nucleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.896763
Cortical amygdalar area, posterior part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.0307
outer portion of lateral ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.32791
H3K4me3_megakaryocyte_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_SK-N-SH_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
amygdaloid complex_13 pcw_M_12888	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.25912
H3K9ac_heart_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_10108_KD_EIF4A3_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.06587
E2F1-18555785-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
YY1_GM12891_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_1358_KD_GANAB_SRP299805	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.89074
NEUROD1_Deficiency_GDS3000_612_mouse_Pineal glands of neonates	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
H3K9ac_liver_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_6005_KD_CHAF1A_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	18.2291
Primary pulmonary hypoplasia_Lung Tissue_GSE1363	GEO Signatures of Differentially Expressed Genes for Diseases	-1.0	-1.54805
H3K4me3_CH12.LX_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
GSE223908,GSE223909_1_v_8_serpinb3_human	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-3_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
WRNIP1	ENCODE Transcription Factor Targets	1.0	null
CUX1	ChEA Transcription Factor Targets	1.0	null
OVCAR-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.930385
Prostate adenocarcinoma_PRAD_TCGA-G9-6363-01A-21R-1789-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_liver_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
PML_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2AphosphoS5_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
integral component of membrane	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
Perturb_8851_KD_MLKL_SRP165226	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.48815
H3K4me3_lung_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
HCC1569	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	-1.0	-2.56819
POLR2A_HepG2_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE198380_0_v_1_phgdh_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me1_liver_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8188_KD_HNRNPC_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.20557
SUM1315MO2	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	0.814221
Perturb_2356_KD_IRX6_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.45864
G141	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.18605
GSE162276_2_v_3_pparg_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Gata-6_KO_GDS4782_330_mouse_Adult heart during pressure overload	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
HDAC6	ENCODE Transcription Factor Targets	1.0	null
Cervical cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.472
PMC7818749-12931_2021_1617_MOESM1_ESM.xlsx-TBX4-SYMBOL_TBX4	Rummagene Transcription Factor Associations 2026	1.0	null
SETDB1_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-FR-A7U9-06A-11R-A352-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Neoplasms	CTD Gene-Disease Associations	1.0	1.11116
GSE189789_0_v_1_oridonin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Sarcoma_SARC_TCGA-DX-A48N-01A-11R-A30C-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_18448_KD_PHF14_SRP199105	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.3115
Perturb_2521_KO_HSF1_SRP341615	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.57944
Perturb_360_KD_CCDC50_SRP349176	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.48238
Perturb_8886_OE_FOXM1_ERP109084	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.15866
Perturb_4490_KO_Pantr2_SRP390021	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	1.69903
Perturb_2468_OE_MIR193BHG_SRP268862	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.97197
REST_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Systolic Pressure	DisGeNET Gene-Phenotype Associations	1.0	null
Perturb_14068_KD_ALKBH5_SRP247667	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_7354_OE_TUT7_SRP120600	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.00967
NCI-H2172	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.57339
Cortical amygdalar area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.03468
H3K9ac_Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_12356_KD_PRPF8_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.69316
GSE216394_2_v_0_pfkp_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE129389_0_v_7_tropifexor_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_14202_KD_KLF5_ERP117894	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.09758
tissues, cell types and enzyme sources	TISSUES Experimental Tissue Protein Expression Evidence Scores	1.0	1.53602
Uterine Carcinosarcoma_UCS_TCGA-N5-A4RO-01A-11R-A28V-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE202434,GSE202438_12_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
parvocellular part of r8LRt	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.90041
bone marrow	HPA Tissue Protein Expression Profiles	-1.0	-1.44043
Perturb_3881_OE_HLAC_SRP363812	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.55188
Perturb_13939_KO_USP29_SRP329795	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Lung adenocarcinoma_LUAD_TCGA-44-2665-01A-01R-0946-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
dorsolateral prefrontal cortex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.53459
Mouth floor	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.571
PMC8134690__F1	PFOCR Pathway Figure Associations 2024	1.0	null
FOXM1	ENCODE Transcription Factor Targets	1.0	null
Perturb_9815_KD_UTX_SRP062773	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.01818
Perturb_2775_KD_TSHZ3_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.78652
intermediate part of THyB	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.14599
GSE89018_1_v_8_cry2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
TEAD4_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Acute Myeloid Leukemia_LAML_TCGA-AB-2917-03A-01T-0734-13	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_12571_KD_YBX1_SRP262465	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.01005
NB1	CCLE Cell Line Gene CNV Profiles	-1.0	-2.07205
Perturb_2976_KD_ZFX_SRP115395	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.24219
CTCF_GM12873_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Periventricular hypothalamic nucleus, posterior part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.58239
PMC11982601-IMM-175-84-s005.xlsx-Fig5D_LPS-Innate_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
KMS-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.22315
TBP_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CHAGOK1	CCLE Cell Line Gene Expression Profiles	1.0	1.36718
substantia nigra, pars reticulata, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.886397
Dmrt1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	24.4058
SNU-C5	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.592
496100484_FWM_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.22458
Perturb_6042_KD_MYEF2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me3_G1E-ER4_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
DIS3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.12639
r7 part of cochlear column	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.12984
Perturb_4341_OE_MYT1L_SRP271657	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.37069
NFIL3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.0188
Papillary thyroid cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.726
POLR2A_GM18526_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
werirb1	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.836
19168792-TableS3	GeneSigDB Published Gene Signatures	1.0	null
GTEX-T6MN-0011-R6A-SM-32QP8	GTEx Tissue Sample Gene Expression Profiles	1.0	1.43348
GSE264621_1_v_3_secretin_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_5414_KD_SCRIB_SRP300624	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.54032
MYBL2_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Pancreatic adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.132
PMC5651844-41467_2017_1173_MOESM5_ESM.xlsx-Down_genes_shY2-1-Supplementary_Data_1_Down_regulated_genes_in_ShY2_KD_cells_AR	Rummagene Transcription Factor Associations 2026	1.0	null
amygdaloid complex_16 pcw_M_12837	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.955678
PML_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Liver cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.69
OVCAR-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.98583
PMC9823215-mmc4.xlsx-Sheet1-List_of_genes_commonly_upregulated_by_wild_type_and_zinc_finger_mutant_of_LIN28A_LIN28A	Rummagene Transcription Factor Associations 2026	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-HL-7533-01A-11R-2232-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
abnormal retina outer nuclear layer morphology	IMPC Knockout Mouse Phenotypes	1.0	null
Perturb_3713_KO_PIWIL1_SRP188921	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	16.2218
GSE133213_2_v_3_znrf3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
HCC4011	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.866753
KLF4-19030024-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_6468_OE_PROX1_ERP110083	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.07681
Perturb_4352_KD_EP300_SRP068733	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.65287
YY1_HCT116_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
UACC-257	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
Esophageal disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.226
PMC7468443-Data_Sheet_2.xlsx-DEG_2h_LPS-Unnamed_7_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_8090_KD_HNRNPL_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE158456_1_v_3_furin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Stomach carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.017
CCDC88B	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.52977
H3K4me2_mammary epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
SP1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_364_KO_PTPN2_SRP108032	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.31033
Esophageal epithelium	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.752
H3K4me3_cardiac mesoderm_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
SNU-423	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	DisGeNET Gene-Disease Associations	1.0	null
GSE89018_11_v_8_cry2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_17466_KO_Prm7_SRP067359	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	2.72887
Adult Fibrosarcoma	DisGeNET Gene-Disease Associations	1.0	null
H3K4me3_Caco-2_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_HCT116_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZBTB7A_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE134316_1_v_0_mtor_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Retinoblastoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.097
Perturb_11542_OE_KRAS_SRP175175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.23379
GSE62974_1_v_0_epas1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
YY1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_754_OE_METTL3_SRP393226	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
BCLAF1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GABPA	ENCODE Transcription Factor Targets	1.0	null
GTEX-NPJ8-1526-SM-2D7VU	GTEx Tissue Sample Gene Expression Profiles	1.0	1.10735
PMC3371315-NIHMS350140-supplement-8.xls-MCF7-T47D-SK-453_Down_MCF7-T47D-Supplementary_Table_1_ER-positive_FOXA1_signature_Genes_decreased_only_in_MCF7_and_T47D_cells_with_knockdown_of_FOXA1_FOXA1	Rummagene Transcription Factor Associations 2026	1.0	null
Mobilized_CD34_Primary_Cells_Female	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	1.0	1.34727
SALL3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.09955
GSE222103_0_v_1_ybx1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE92364_0_v_5_asparaginase_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
POU2F1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.7881
ATRFLOX	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.9794
Adrenocortical carcinoma_ACC_TCGA-OR-A5JM-01A-11R-A29S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Olanzapine_LOX-IMVI	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0067593
hippocampus (hippocampal formation)_12 pcw_F_13060	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.90248
H3K4me1_Stomach Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
layer 3 of PaS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.2439
GTEX-X4XX-0011-R2A-SM-3P623	GTEx Tissue Sample Gene Expression Profiles	1.0	2.6047
Perturb_14582_KO_NQO1_SRP217327	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.51128
ABC1	CCLE Cell Line Gene CNV Profiles	1.0	1.63836
H3K4me3_HepG2_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
hsa-miR-497	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.07142
SNU1214	CCLE Cell Line Gene CNV Profiles	1.0	1.76051
GSE223908,GSE223909_1_v_3_serpinb3_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_8788_KO_HNF6_SRP217514	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.21818
GSE184884_2_v_1_gps2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC4266008-mmc3.xlsx-iPS-MSC_vs_MSC-Unnamed_1_MSC	Rummagene Transcription Factor Associations 2026	1.0	null
KMRC3	DepMap CRISPR Gene Dependency	1.0	2.52884
ZNF354A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	79.9426
POLR2A_K562_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Leukemia	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.366
HCC4017	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38117
GSE157555,GSE157556_3_v_2_foxa2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
TBX4-33478486-IMR90-HUMAN-LUNG	ChEA Transcription Factor Targets 2022	1.0	null
H3K27ac_mammary epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_2054_KD_CHERP_SRP354316	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
TAF1	ENCODE Transcription Factor Targets	1.0	null
Perturb_6456_KO_GCN2_SRP346390	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.68599
dorsal entopeduncular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.5267
anterior (rostral) cingulate (medial prefrontal) cortex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.56352
Perturb_13440_KD_MLLAF9_SRP119047	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	20.0
GSE233679_5_v_7_nicotinamide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
regulation of i-kappab kinase/nf-kappab signaling	GO Biological Process Annotations 2015	1.0	null
POLR2A_bone marrow_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-HT-7602-01A-21R-2090-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE215086_3_v_7_batf_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Primary somatosensory area, upper limb, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.27056
TBP_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
negative regulation of intracellular signal transduction	GO Biological Process Annotations 2015	1.0	null
MAX_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
lateral orbital frontal cortex (area 12/47)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.6129
hsa-miR-4652-3p	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.843347
Neoplasm Metastasis	DisGeNET Gene-Phenotype Associations	1.0	null
Perturb_10256_KD_TP53_SRP346937	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.74002
GSE142210_4_v_8_panobinostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE178532_2_v_0_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K4me3_HEK293_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
VZ in medial temporal-occipital cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.33705
RAD21_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9165_KD_circCAMSAP1_SRP366297	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.30921
Heart	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-1.40139
Perturb_448_KO_RPA_SRP158719	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
intracellular membrane-bounded organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
H3K9ac_IMR90	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
ETS1	ENCODE Transcription Factor Targets	1.0	null
Perturb_8869_KD_PNN_SRP063860	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.96135
CTCF_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TBP_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZMIZ1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TCC-SUP cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.861
MYF6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.088
105KC	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.30158
HCC1937	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	1.38185
H3K4me3_fibroblast of foreskin _hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
C2BBE1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.904017
negative regulation of biological process	GO Biological Process Annotations 2015	1.0	null
Perturb_8094_KD_PUM2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.1421
H3K4me3_SK-N-MC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_17690_KD_MDMX_SRP393452	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_550_KD_EWSR1FLI1_SRP273158	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.52704
Perturb_9417_KD_Mecom_SRP356893	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	1.47444
GSE120612_7_v_3_etoposide_human	RummaGEO Drug Perturbation Signatures	1.0	null
NCI-H146	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.1117
Perturb_8199_KD_CALR_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.7255
GSE178227_1_v_0_tet1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC9290241-13058_2022_1547_MOESM2_ESM.xlsx-Foglio1-Supplementary_Table_S1_Differentially_expressed_transcripts_in_common_between_EPZ-_and_MI-2-treated_MCF-7_cells_MITF	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_9982_KD_SF3B4_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.65524
NCIH2172	CCLE Cell Line Gene CNV Profiles	-1.0	-1.60384
TAF1_HepG2_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE180185_4_v_5_setbp1_human	RummaGEO Gene Perturbation Signatures	1.0	null
CEBPB_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-22-4613-01A-01R-1443-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-NC-A5HR-01A-21R-A26W-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Lymphoma_burkitts(Raji)	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-1.92491
YY1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SOX10	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.5178
Perturb_9883_KD_CPEB4_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.72034
bone marrow	HPA Tissue Gene Expression Profiles	1.0	0.924359
suz12_17339329_mouse_embryonic_stem_cell_es_cell_lof_mouse_gpl1261_gse31354	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.49586
GSE227592_4_v_3_adar_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE154577_13_v_10_plagl1_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE201217_4_v_6_usf2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
OLIG1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.977
PMC5554756__F2	PFOCR Pathway Figure Associations 2023	1.0	null
Perturb_8462_KO_IFNLR1_ERP121014	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.50556
Perturb_478_KD_PPARGC1A_SRP278736	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.22332
PABPC1L	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.40811
EEF1AKMT4	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.98414
Adult_Liver	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	-1.0	-1.33867
CD33+_Myeloid	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-0.976858
layer 3 of FCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.89588
CRY2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.44324
FOSL2	ENCODE Transcription Factor Targets	1.0	null
GSE118617,GSE118619_0_v_1_foxp1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Urinary system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.447
Perturb_8095_KD_SLBP_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K4me3_fibroblast of villous mesenchyme_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_choroid plexus epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Pallidum, dorsal region	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.20528
Perturb_8753_KD_ANLN_SRP083014	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
POLR2A_limb_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6055_KD_PTBP1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
POLR2AphosphoS2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A2JA-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_4260_OE_MEIS1_SRP201342	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.61576
GSE168458_1_v_3_disulfiram_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_2064_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.10825
Pheochromocytoma and Paraganglioma_PCPG_TCGA-P7-A5NY-01A-12R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE223008_5_v_1_calhm6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE68156_0_v_5_dextran_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
POLR2A_GM12891_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
regulation of signal transduction	GO Biological Process Annotations 2015	1.0	null
EP300_GM12878_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
gata1_15860665_megakaryocytes_lof_mouse_gpl1261_gds1245	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.505873
H3K9ac_astrocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Orbital area, lateral part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.14523
Primary effusion lymphoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.518
absent mesoderm	MGI Mouse Phenotype Associations 2023	1.0	null
hsa-miR-2278	TargetScan Predicted Conserved microRNA Targets	1.0	0.059817
Perturb_1310_KO_Cntnap4_SRP387040	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-4.81381
Endoplasmic reticulum	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	1.0	4.0
CTCF_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Rectum adenocarcinoma_READ_TCGA-DC-6682-01A-11R-1830-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Medulloblastoma	DisGeNET Gene-Disease Associations	1.0	null
PMC6151027-12864_2018_5080_MOESM3_ESM.xlsx-E20-D3_1775_AR-DEGs-Symbol_AR	Rummagene Transcription Factor Associations 2026	1.0	null
POLR2AphosphoS2_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE211286_1_v_3_tcf12_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-DK-A6B5-01A-11R-A31N-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H2AFZ_mammary epithelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44043
GSE147662_0_v_1_nicotinamide_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
hsa-miR-607	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
FOXM1-25889361-OE33-AND-U2OS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
GSE217115_2_v_0_alectinib_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
TIA1_KO_GSE54418_260_mouse_cerebellum	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
Perturb_8227_KD_HDGF_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.38813
Perturb_14104_KD_HNRNPC_SRP274546	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.77979
Everolimus_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0275287
Perturb_12492_KD_PELP1_SRP351131	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.9768
GSE149903_3_v_2_myd88_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE119978,GSE180930_6_v_1_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-A49C-01A-11R-A24H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_12496_KD_TP53_SRP364608	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.52125
GSE169356_0_v_1_ivermectin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-QVJO-1426-SM-2S1QY	GTEx Tissue Sample Gene Expression Profiles	1.0	1.30868
H3K27ac_fibroblast of dermis_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
PML_MCF-7_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14129_KD_AKR1B1_SRP400403	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.732
OVCAR-3 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.823
FOXP4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.9793
GSE113734_1_v_2_qprt_human	RummaGEO Gene Perturbation Signatures	-1.0	null
TCF12_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
RPL38	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.39621
GSE197630_1_v_0_ruvbl1_human	RummaGEO Gene Perturbation Signatures	1.0	null
POLR2A_endothelial cell of umbilical vein_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TIA1_KO_GSE54418_267_mouse_spinal cord	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
GSE139348,GSE139349_1_v_0_dicer1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE130956_2_v_1_icaritin_human	RummaGEO Drug Perturbation Signatures	1.0	null
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1657
Perturb_7375_KD_PUF60_ERP105778	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.46536
Perturb_1120_KD_CCND3_SRP325057	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.55203
TAL1::TCF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.9773
Lung squamous cell carcinoma_LUSC_TCGA-O2-A52S-01A-11R-A262-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE110708_0_v_3_adar_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_GM12864_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_12676_KO_PTPN2_SRP108032	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.46406
Perturb_6711_KD_STAU1_SRP266909	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.19613
Perturb_15421_KD_ELL2_SRP214471	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.9797
TRIM28	ENCODE Transcription Factor Targets	1.0	null
16151515-TableS3	GeneSigDB Published Gene Signatures	1.0	null
NCI-H810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.39575
Perturb_13534_KO_HDGFL2_SRP153901	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.40991
Perturb_317_KD_TP63_SRP353945	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
ChIP_CNOT3_19339689	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
TALL1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.33315
fastigial nucleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.38716
Colorectal Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
GSE192689_0_v_1_ricin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
TAF7_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15798_KD_EMP2_SRP265560	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.4057
KDM5B-21448134-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
r1 roof plate	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.33452
GSE149035_1_v_0_hepacam_human	RummaGEO Gene Perturbation Signatures	-1.0	null
POLR2A_endothelial cell of umbilical vein_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_embryonic fibroblast_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
external globus pallidum	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.38906
BICR78	DepMap CRISPR Gene Dependency	1.0	2.02627
Globus pallidus, internal segment	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.35369
JUND_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
layer 5 of PaS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.75901
Sarcoma_SARC_TCGA-WK-A8XS-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
hsa-miR-3074-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
layer 6b of RSC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.14149
Left_Ventricle	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	-1.0	-0.981032
H3K4me2_B cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K9me3_GM12878_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
REST_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NFYB	ENCODE Transcription Factor Targets	1.0	null
SW48	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Perturb_8097_KD_SUCLG1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.2419
Perturb_8085_KD_DAZAP1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
IL11RA	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.11821
Perturb_4372_KD_SUZ12_SRP071040	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.72928
GSE228413_2_v_1_mavs_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
UTP6	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.34771
GSE209911_0_v_1_ncstn_human	RummaGEO Gene Perturbation Signatures	1.0	null
H3K9ac_fibroblast of dermis_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
TRIM28_HEK293_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_GM12875_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_brain_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_fibroblast of mammary gland_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K27me3_cardiac mesoderm_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2389_KD_NSD3_SRP267458	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.8642
H3K4me3_fibroblast of foreskin _hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
STAT5A_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Piriform-amygdalar area, pyramidal layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.38842
RELA_GM15510_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE226316_3_v_2_tead2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_2795_KD_PSMD2_SRP173284	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.75068
GSE226249_5_v_3_pirfenidone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-NPJ7-0011-R8a-SM-2I3G2	GTEx Tissue Sample Gene Expression Profiles	1.0	1.63887
Liver Cirrhosis, Experimental	DisGeNET Gene-Disease Associations	1.0	null
non-small cell lung adenocarcinoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.424
MAFF	ENCODE Transcription Factor Targets	1.0	null
H3K4me3_epithelial cell of proximal tubule_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_14327_KD_TIGAR_ERP111405	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
liver_c	HPA Tissue Sample Gene Expression Profiles	-1.0	-0.875447
MDST8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.913371
H3K4me1_kidney_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7498_KO_USP10_SRP192777	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.6158
Tcf1_KO_GDS1473_307_mouse_Pancreatic islets	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GSE246195,GSE246305_2_v_0_sin3a_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
globus pallidus, internal segment, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.43697
PMC9675280-12950_2022_317_MOESM3_ESM.xlsx-siPAD2_LPS_vs_siCON_LPS-Unnamed_1_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
POU2F2_GM12891_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
primary visual cortex (striate cortex, area V1/17)_3 yrs_F_12836	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.28782
Perturb_2350_KD_BNC2_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Cortical amygdalar area, posterior part, lateral zone, layer 2	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.03204
DOR 13	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.26592
COVID-19	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.284
PDCD2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.26793
Perturb_9146_KD_LRRC8A_SRP306897	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.39785
H3ac_myocyte_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
RCOR1_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TCF12_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE179974_3_v_5_carboplatin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE248045,GSE248046_6_v_5_runx1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
POLR2A_olfactory bulb_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6029_KD_KHDRBS3_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Liver hepatocellular carcinoma_LIHC_TCGA-CC-A3M9-01A-11R-A213-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HDAC6_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE193402_0_v_3_imatinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me3_H7_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
ESR2	Hub Proteins Protein-Protein Interactions	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-HC-A631-01A-11R-A29R-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
paraventricular nucleus of the hypothalamus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.07893
GSE87404,GSE87812_1_v_3_hoxa9_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
oral mucosa	HPA Tissue Protein Expression Profiles	1.0	1.24946
Perturb_554_KD_KDM5A_SRP277893	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
496100626_FWM_no dementia_TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.28172
Primary motor area, Layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.25439
H3K4me1_Skeletal Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
ChIP_TCFCP2L1_18555785	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
GSE172295_4_v_2_sh3gl1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
POLR2A_testis_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Pharynx cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.106
COLO680N	CCLE Cell Line Gene CNV Profiles	1.0	2.13447
GSE178714_5_v_0_smad2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-E7-A85H-01A-11R-A352-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC10771438-41598_2023_51082_MOESM1_ESM.xlsx-Day21-Supplementary_Dataset_1_List_of_genes_differentially_expressed_during_NS_PC_differentiation_between_ROR2_KD_cells_and_control_cells_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_6521_KD_HES3_SRP162877	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.55048
MAX_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE146074_9_v_7_ly6e_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
ABC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.01687
Cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	2.113
AML193	CCLE Cell Line Gene Expression Profiles	-1.0	-1.50975
Musculoskeletal system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.207
Mouth	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
Kidney renal papillary cell carcinoma_KIRP_TCGA-B9-4115-01A-01R-1193-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GATA1_G1E-ER4_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-R55E-0011-R8A-SM-2TC66	GTEx Tissue Sample Gene Expression Profiles	1.0	1.82385
Perturb_8048_KD_METTl14_SRP167173	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.3878
JUN_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me1_lung_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Uterine cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.486
Perturb_6432_OE_RBFOX1_SRP372391	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
POLR2AphosphoS5_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-Q2AG-0011-R7A-SM-2HMJP	GTEx Tissue Sample Gene Expression Profiles	1.0	1.83504
Perturb_628_KO_HOXD3_ERP117895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.22544
inner SZ in primary visual cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.24321
NFYA	ENCODE Transcription Factor Targets	1.0	null
Crus II, right, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.977596
CTCF_foreskin fibroblast_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-NPJ7-0011-R2a-SM-2I3GF	GTEx Tissue Sample Gene Expression Profiles	1.0	2.50686
intracellular membrane-bounded organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
Male reproductive organ cancer	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
Vascular disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.262
ZNF449	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.3311
Perturb_2432_KD_PRRX1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.4878
Perturb_10000_KD_CPSF6_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.6769
POLR2A_heart_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CBX3_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_HCT116_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_12309_KD_METTL14_SRP074429	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.15512
Skin Cutaneous Melanoma_SKCM_TCGA-EB-A5VV-06A-11R-A32P-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE128730_4_v_2_neratinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Face	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	2.0
Perturb_11433_KD_NKX25_SRP152523	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.2459
MAFK_IMR-90_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC9941047-41591_2022_2163_MOESM3_ESM.xlsx-ST12-Unnamed_1_KLF6	Rummagene Transcription Factor Associations 2026	1.0	null
CTCF_GM12864_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
cytoplasm	LOCATE Predicted Protein Localization Annotations	1.0	null
Perturb_12688_KD_USP34_SRP150508	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.34422
MAX_A549_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
KAT2B_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
AKIRIN1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.06752
TT	CCLE Cell Line Gene CNV Profiles	1.0	1.53303
Human - Motor Cortex - Cluster - OPALIN+ LRP4-AS1+ Layer 3-6 oligodendrocyte	HuBMAP Azimuth Cell Type Annotations	1.0	null
Crus II, left, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.07707
GSE231745_1_v_0_venetoclax_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Sox5	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	17.6532
abnormal embryo development	MGI Mouse Phenotype Associations 2023	1.0	null
CTCF_GM12872_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE164505,GSE164506_3_v_2_indisulam_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Superior central nucleus raphe, lateral part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.48804
navicular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.11621
Perturb_15874_KO_ATF6_SRP401118	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.99462
Neuroblastoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.314
Hyperplasia	CTD Gene-Disease Associations	1.0	1.13689
NFYB_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
REST_01_337	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.5851
GSE89018_11_v_14_cry2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
r2 part of prepontine raphe nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	3.17341
Perturb_2767_KD_CTBP1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
NCIH2347	CCLE Cell Line Gene Expression Profiles	1.0	2.27603
Gastric epithelial cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.822
SATB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	34.417
Perturb_8145_KD_AKAP8_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.64753
SARS-BatSRBD_84Hour_23935999_GSE47962	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.66057
GSE208254_3_v_2_irf8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NRF1	JASPAR Predicted Transcription Factor Targets	1.0	null
GABPA_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
medial geniculate complex, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.02162
PAX5	ENCODE Transcription Factor Targets	1.0	null
Perturb_5646_KD_LOXHD1_SRP298159	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.16583
Buccal epithelium	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.84
EP300_T47D_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_7437_KO_YTHDF2_SRP082495	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.41321
ZMIZ1	ENCODE Transcription Factor Targets	1.0	null
CREM	ChEA Transcription Factor Targets	1.0	null
POLR2A_MCF 10A_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ONECUT1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.8547
CTCF_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TBP_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3517_KD_RBM8A_ERP130710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
pancreas	HPA Tissue Gene Expression Profiles	-1.0	-0.881916
GSE242083,GSE242098_3_v_0_med1_human	RummaGEO Gene Perturbation Signatures	1.0	null
CTCF_mammary epithelial cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_foreskin fibroblast_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_HeLa-S3_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE228181_4_v_5_idh1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
decreased total retina thickness	MGI Mouse Phenotype Associations 2023	1.0	null
H3K4me3_GM12864_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HNF1A-27111144-CD8+TCELLS-MOUSE-BLOOD-LYMPHOMA	ChEA Transcription Factor Targets 2022	1.0	null
H3K4me3_heart_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8038_KO_FOXA2_SRP350523	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.8389
GSE186810,GSE186813_7_v_0_furin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Clonidine (hydrochloride)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0250166
GSE129244_3_v_1_lmo2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
VZ in caudal subicular cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.25334
JUND_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_1041_Mut_C15orf48_SRP289006	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.89546
NFATC1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
preweaning lethality, incomplete penetrance	IMPC Knockout Mouse Phenotypes	1.0	null
Reproductive system disease	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
ZNF678	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	3.34909
hsa-miR-4477a	TargetScan Predicted Conserved microRNA Targets	1.0	0.436802
H3K4me3_epithelial cell of esophagus_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
HCC1500	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	0.59768
496100596_FWM_dementia_TBI_89_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.15771
Globus pallidus, external segment	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.20381
Perturb_9288_OE_KRAS_SRP172671	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.63174
Perturb_8955_Mut_RB1_SRP220467	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Acute promyelocytic leukemia	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.033
Brain Lower Grade Glioma_LGG_TCGA-E1-A7YK-01A-11R-A34F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_14896_KO_H13_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.0759
Blastopore	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.639
Imago	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.996
GSE199204,GSE211619_4_v_6_glutamine_human	RummaGEO Drug Perturbation Signatures	1.0	null
A4/FUK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.55124
Perturb_12369_KD_POLE_SRP286423	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	12.0306
STAT3_MCF 10A_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-CS-5395-01A-01R-1470-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HCC15	CCLE Cell Line Gene CNV Profiles	-1.0	-1.62632
GSE161295_4_v_3_cdk8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_7541_KO_NSUN6_SRP273753	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.717
GSE180377_2_v_1_lipa_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
mouse	GeneRIF Biological Term Annotations	1.0	null
ISTMES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.83398
PMC8851354-Table_2.xlsx-Genes_reg_by_FUS-DDIT3-Supplementary_Table_2_Genes_significantly_regulated_by_FUS-DDIT3_expression_in_HT1080_cells_adjusted_p-value_0_05_and_log2_Fold_change_1_or_-1_DDIT3	Rummagene Transcription Factor Associations 2026	1.0	null
MEF2A_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8129_KD_DDX3X_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_9633_KD_CHD8_SRP047233	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.53158
CTCF_GM12878_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_CH12.LX_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
posteroventral (inferior) parietal cortex_36 yrs_M_12302	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.856898
Head and Neck squamous cell carcinoma_HNSC_TCGA-CR-5248-01A-01R-2016-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_astrocyte of the cerebellum_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_HeLa-S3_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NRF1	ENCODE Transcription Factor Targets	1.0	null
YY1_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE216273,GSE216292_0_v_6_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
537 MEL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.01275
muscle	GTEx Tissue Gene Expression Profiles	1.0	1.09814
Kidney renal papillary cell carcinoma_KIRP_TCGA-A4-7915-01A-11R-2204-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2059_KD_CHERP_SRP354316	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.87184
POU2F2_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_17200_OE_JUN_SRP188712	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.17278
NCI-H2081	COSMIC Cell Line Gene Mutation Profiles	1.0	null
H3K4me3_GM06990_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8184_KD_DHX30_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.16095
lymphnode_4a	HPA Tissue Sample Gene Expression Profiles	1.0	1.11172
Perturb_2438_KD_ZNF589_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.05435
Head and Neck squamous cell carcinoma_HNSC_TCGA-BA-A4IH-01A-11R-A266-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me2_osteoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_12118_KO_FOXA2_SRP350523	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.43105
Perturb_8157_KD_GPKOW_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE155305_3_v_0_ifitm3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE202434,GSE202438_13_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
DERL2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.01084
TBL1XR1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-YL-A8S8-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE111247_11_v_4_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
POU2F2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
EP300_GM12878_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE158632_3_v_1_oxyquinoline_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MYBL1-21750041-SPERMATOCYTES-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
JUND	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.6895
POLR2A_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2A_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H727	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.21214
Medial amygdalar nucleus, posteroventral part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.46785
GTEX-P44H-0011-R8A-SM-2XCEL	GTEx Tissue Sample Gene Expression Profiles	1.0	1.19081
Perturb_2051_KD_EIF4A3_SRP271455	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.55528
H3K4me1_embryonic fibroblast_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
ethanol_rattus norvegicus; unidentified_gpl2000_gse2718	GEO Signatures of Differentially Expressed Genes for Small Molecules	-1.0	null
endoplasmic reticulum	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
hsa-miR-371-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.40969
Perturb_711_KO_DNMT3B_SRP389363	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.49805
PMC9574515-mmc1.xls-THP1_60_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
ELK1::HOXB13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5447
NELFE	ENCODE Transcription Factor Targets	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-CH-5754-01A-11R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE158815_1_v_3_trib1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
CLC	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.23429
EP300_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Sox17	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	19.6474
Perturb_11431_OE_YAP/FOSL1_SRP360169	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.96748
GSE184884_4_v_1_gps2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE162590_1_v_0_gsx2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GTEX-T6MN-0011-R5A-SM-32QPD	GTEx Tissue Sample Gene Expression Profiles	1.0	0.98722
Childhood Medulloblastoma	DisGeNET Gene-Disease Associations	1.0	null
failure of primitive streak formation	MGI Mouse Phenotype Associations 2023	1.0	null
central medullary reticular group, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.966741
H3K4me3_fibroblast of lung_hg19_6	ENCODE Histone Modification Site Profiles	1.0	null
GSE179974_3_v_2_carboplatin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Taenia tecta, ventral part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.82286
RFX5_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_623_KO_SLFN11_SRP233180	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.07066
Intrahepatic cholangiocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.03
Perturb_6045_KD_NONO_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
PPP2R5E	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.05425
GSE131798,GSE131804_2_v_0_igf1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
496100436_FWM_no dementia_no TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.56097
Zinc finger, RING/FYVE/PHD-type	InterPro Predicted Protein Domain Annotations	1.0	null
Perturb_9063_KD_NANOG_SRP100928	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.0996
SMC3_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TEAD4	ENCODE Transcription Factor Targets	1.0	null
Perturb_10105_KD_DDX3X_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.23723
Perturb_3641_KO_BRD9_ERP115567	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.84032
POLR2A_HCT116_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CEBPB_A549_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_epithelial cell of proximal tubule_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8161_KD_SF3B1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.87621
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-C5-A7CK-01A-11R-A32P-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_16004_OE_HOXA13_SRP107176	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.36561
Autoimmune disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.036
Perturb_2075_KD_PUM1_SRP072710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.16846
Prelimbic area, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.43114
Primary somatosensory area, trunk, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.20404
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A1Q9-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE134214_0_v_1_ell2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Digestive gland	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
rostral division of OFCi (area 11)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.984345
parataenial nucleus of thalamus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-2.72771
GSE179974_3_v_4_carboplatin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE86507,GSE86509_4_v_8_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Uterine Carcinosarcoma_UCS_TCGA-N8-A4PO-01A-11R-A28V-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE133683_1_v_5_doxorubicin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
CTCF_BE2C_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9892_KD_PPIG_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.68827
Malignant Neoplasm	DisGeNET Gene-Disease Associations	1.0	null
primary motor-sensory cortex (samples)_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.54492
NELFE_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_HepG2_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE164757,GSE164759_1_v_2_trametinib_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
ATF2	ENCODE Transcription Factor Targets	1.0	null
GSE119978,GSE180930_6_v_4_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE235701,GSE261434_2_v_1_enasidenib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
NELFE_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8822_KD_TRRAP_SRP106050	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.42231
V	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.19257
GSE168076,GSE168080_1_v_0_batf_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE133691_2_v_0_lgr5_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
primary motor cortex (area M1, area 4)_1 yrs_F_12830	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.19344
UBTF_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE229468,GSE229471_0_v_1_znf587_human	RummaGEO Gene Perturbation Signatures	1.0	null
Cholangiocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.436
Osteosarcoma	DisGeNET Gene-Disease Associations	1.0	null
H3K9ac_Colonic Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Pancreas	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
ZEB1	ENCODE Transcription Factor Targets	1.0	null
H3K4me3_Duodenum Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_13776_KD_IFNAR2_SRP329434	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.11329
NCOR1	ENCODE Transcription Factor Targets	1.0	null
Perturb_7798_KD_UPF1_SRP063462	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.69431
Perturb_10011_KD_AARS1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.55598
GSE146074_10_v_7_ly6e_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Eye disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.112
GSE178255_3_v_6_tlr4_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_15008_KD_Klf5_SRP341620	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-6.40887
hsa-miR-107	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.07142
GSE235682_1_v_0_rbl2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE132948,GSE132949_2_v_5_msi2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
859_BMS1_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.727244
KYSE-180	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	2.11314
reuniens nucleus (medioventral nucleus) of thalamus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-2.0579
POLR2A_GM19193_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
RNF2	ENCODE Transcription Factor Targets	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-HT-7479-01A-11R-2027-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE169356_0_v_5_ivermectin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_9088_KD_SUPT16H_SRP106869	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.38286
Prostate cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.707
LC1SQSF	CCLE Cell Line Gene Expression Profiles	1.0	2.07435
PANC-04-03	COSMIC Cell Line Gene Mutation Profiles	1.0	null
H3K4me3_fibroblast of lung_hg19_4	ENCODE Histone Modification Site Profiles	1.0	null
H3K9ac_CH12.LX_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
ADRM1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.15711
GSE114690_2_v_3_tnfsf14_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Minor Salivary Gland	GTEx Tissue Gene Expression Profiles 2023	1.0	0.911262
GSE210682_0_v_3_methadone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE178714_1_v_4_smad2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
HDAC2_H1-hESC_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Liver Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
GSE230354_0_v_1_rheb_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
KP-N-YN	COSMIC Cell Line Gene Mutation Profiles	1.0	null
2339_DPCD_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.522838
hsa-miR-499-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
MYC_01_324	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.60328
Kidney renal clear cell carcinoma_KIRC_TCGA-BP-4325-01A-02R-1289-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE87404,GSE87812_1_v_0_hoxa9_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-DK-A1AC-01A-11R-A13Y-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_MCF-7_hg19_8	ENCODE Transcription Factor Binding Site Profiles	1.0	null
eGFP-JUND_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_691_KD_PTPN6_SRP275597	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE135352_0_v_1_napabucasin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
layer 5 of PrS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.31077
Adenocarcinoma	DisGeNET Gene-Disease Associations	1.0	null
hsa-miR-2116	TargetScan Predicted Conserved microRNA Targets	1.0	0.257113
Perturb_13682_KD_METTL14_SRP103115	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.22805
GTEX-WHSE-2926-SM-3NMBG	GTEx Tissue Sample Gene Expression Profiles	1.0	1.24515
LU99	CCLE Cell Line Gene Expression Profiles	1.0	1.3505
hsa-miR-4698	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
GSE155305_2_v_0_ifitm3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_6088_KD_YBX1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GTEX-RU72-0011-R2A-SM-2TF6O	GTEx Tissue Sample Gene Expression Profiles	1.0	1.36731
GSE240386,GSE242143_1_v_3_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
Orbital area, medial part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.0691
Perturb_13601_KD_YAP1_SRP337871	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.35424
SLC25A4	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.32739
Perturb_13756_KD_KLF4_SRP233218	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.44208
Perturb_8301_KD_ETF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.6688
MAFF_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_bone marrow macrophage_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_12850_KO_Tet2_SRP338315	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	9.60676
POU2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.2679
EW1	DepMap CRISPR Gene Dependency	1.0	8.8601
Liver hepatocellular carcinoma_LIHC_TCGA-BW-A5NP-01A-11R-A27V-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Forced Expiratory Volume Function	DisGeNET Gene-Phenotype Associations	1.0	null
Perturb_2349_KD_PBRM1_SRP381930	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	13.3608
Perturb_15432_KD_CSN5_SRP316687	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-15.0229
CHD2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K23me2_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
decreased total retina thickness	IMPC Knockout Mouse Phenotypes	1.0	null
COV504	CCLE Cell Line Gene CNV Profiles	1.0	1.3534
CW-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	1.0	null
Methylprednisolone succinate_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0150054
Perturb_9313_KD_HOTAIR_SRP378143	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.34739
Whipple's Disease_macrophage_GSE16180	GEO Signatures of Differentially Expressed Genes for Diseases	-1.0	-2.54754
GTEX-T6MN-0011-R9A-SM-32QOZ	GTEx Tissue Sample Gene Expression Profiles	1.0	1.42357
GSE149264,GSE149267_2_v_1_trp53_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
cellular_component	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
frontal pole, left, inferior aspect	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.917667
dorsolateral prefrontal cortex_8 yrs_M_12841	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.06127
Perturb_17202_KD_HOTAIRN_SRP159658	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.9573
GSE254155_5_v_0_per2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
abnormal retina outer nuclear layer morphology	MGI Mouse Phenotype Associations 2023	1.0	null
Perturb_17786_KO_LDBI_SRP071739	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GATA1_G1E-ER4_mm9_9	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-15b	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
RCM1	DepMap CRISPR Gene Dependency	1.0	4.57097
Perturb_8151_KD_SUGP2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.9019
H3K27ac_CD14-positive monocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
hippocampus (hippocampal formation)_13 pcw_M_12888	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.969744
GTEX-WZTO-0011-R8A-SM-4E3II	GTEx Tissue Sample Gene Expression Profiles	1.0	1.05585
MDA-MB-231	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32505
GSE147876,GSE147877_4_v_1_enzalutamide_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_12353_KD_LUC7L2_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.82308
Perturb_6767_Mut_KDM6A_SRP343264	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.11873
limitans nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.75865
Brain Lower Grade Glioma_LGG_TCGA-P5-A5EZ-01A-11R-A27Q-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_3799_KD_ZNF281_SRP377192	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.38356
MAX_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE142210_9_v_7_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
CHD1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14901_KO_H15_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.274
GSE88819_5_v_4_tug1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE169356_0_v_4_ivermectin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_13863_KD_TBX2/MYCN_ERP107244	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.93637
Perturb_2390_KD_HIF1A/HIF2A_SRP308699	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.36849
GSE206779_1_v_3_angiotensin ii_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
mantle zone of r2BM	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.92211
496100401_FWM_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.12922
PMC9509360-41419_2022_5262_MOESM6_ESM.xlsx-Fig_2D_MSC_targeted_RNF4-Down_MSC	Rummagene Transcription Factor Associations 2026	1.0	null
PMC11076560-42003_2024_6230_MOESM5_ESM.pdf-31-HMGA2_HMGA2	Rummagene Transcription Factor Associations 2026	1.0	null
MC116	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.904823
GSE186440,GSE186443_1_v_5_daxx_human	RummaGEO Gene Perturbation Signatures	-1.0	null
CTCF_choroid plexus epithelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8352_KO_ADCY9_SRP320358	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.05402
inferolateral temporal cortex (area TEv, area 20)_30 yrs_F_12290	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.22572
Cancer	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
Perturb_5624_KD_KLF5_SRP307776	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.2134
GSE154767_4_v_5_adam10_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
ADNP-35650610-MESC-MOUSE-STEM-AUTISM	ChEA Transcription Factor Targets 2022	1.0	null
occipital pole, left, superior aspect	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.41608
Perturb_7244_KD_UPF1LL_SRP295982	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.81015
Perturb_1204_KO_Sp2/Sp1_SRP302435	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-6.05508
GSE128730_0_v_5_neratinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
CBX3_HCT116_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
IRF1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE88819_0_v_9_tug1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
REST	ENCODE Transcription Factor Targets	1.0	null
POU5F1B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.2009
GSE86507,GSE86509_3_v_9_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GFUS	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.10975
PAX6-23342162-BETA-FORBRAIN-LENS-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
CTCF_K562_hg19_6	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_365_KO_PTPN2_SRP108032	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.5974
GSE139975_3_v_1_rnf2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Bed nuclei of the stria terminalis, posterior division, strial extension	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.11047
Perturb_15719_KD_Ctcf_SRP173291	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-20.0
PHF8_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2768_KD_FOXD4L6_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	14.1362
GSE172295_0_v_2_sh3gl1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-MA-AA41-01A-11R-A38B-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC11076560-42003_2024_6230_MOESM5_ESM.pdf-31-ENSG00000149948_HMGA2	Rummagene Transcription Factor Associations 2026	1.0	null
occipital neocortex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.6752
Perturb_14020_OE_MIR722_SRP185837	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_12725_KO_MITF_SRP255094	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.14566
GSE111247_2_v_1_temozolomide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_2294_KD_DDX5_SRP139509	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.83728
POU2F3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.1856
Perturb_17769_KD_PPARGC1A_SRP248218	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.59992
Perturb_4540_KD_Bahd1_SRP126769	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-2.08552
JUND_H1-hESC_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8177_KD_RPS3A_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.08325
TBX2-30127528-KELLY-HUMAN-BRAIN-NEUROBLASTOMA	ChEA Transcription Factor Targets 2022	1.0	null
FOXO1::ELK3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.948
abnormal endoderm development	MGI Mouse Phenotype Associations 2023	1.0	null
H3K4me2_fibroblast of dermis_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H2AFZ_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Olanzapine_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.029122
H2BK5ac_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE229973_4_v_7_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
PMC8481886-Table_1.xlsx-A_subsets-UC_MSC_MSC	Rummagene Transcription Factor Associations 2026	1.0	null
layer 1 of InsCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.05013
Perturb_7932_KD_Spt6_SRP132004	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
liver_d	HPA Tissue Sample Gene Expression Profiles	-1.0	-1.13444
Kidney renal clear cell carcinoma_KIRC_TCGA-B0-5092-01A-01R-1420-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2357_KD_PRRX1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
TIA1_KO_GSE54418_261_mouse_midbrain	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
dorsomedial preoptic area, superficial part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.44444
SGC-7901 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.516
Perturb_7619_OE_OspC1_SRP368098	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.83257
GSE88819_7_v_9_tug1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_7754_KO_LATS1/LATS2_SRP281854	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.42967
H3K27ac_H1 Derived Mesenchymal Stem Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
TYK-NU.CP-R	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.17104
GTEX-WHSE-0011-R8A-SM-3P5Z1	GTEx Tissue Sample Gene Expression Profiles	1.0	1.07767
H-1299	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.079
SOX11_DEPLETION_GDS4801_326_human_Z138 mantle cell lymphoma (MCL) cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GSE160817_7_v_6_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Gonadal disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.531
H3K56ac_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_15444_KD_HDAC5_SRP273298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.3629
inner SZ in dorsomedial extrastriate cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.13777
Thoracic disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.789
Necrosis	CTD Gene-Disease Associations	1.0	1.76347
DPRX	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.104
GSE211226_1_v_0_sirpa_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
CDX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.2763
hsa-miR-130b-3p	MiRTarBase microRNA Targets	1.0	null
Perturb_1097_KO_CIC_SRP230198	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.1067
GSE120612_6_v_1_etoposide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Pronephric tubule	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.803
Perturb_12240_KD_CHD4_SRP190500	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.2664
Perturb_4543_KD_Chd4_SRP126769	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-2.16796
amygdaloid complex_17 pcw_F_12880	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.940908
HS578T	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	-1.0	-1.14208
Perturb_8195_KD_SMN1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.89912
GSE166294_0_v_1_etv5_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
primary auditory cortex (core)_13 pcw_M_12820	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.937077
GSE242199_9_v_0_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_cardiac muscle cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
hsa-miR-30b-5p	MiRTarBase microRNA Targets	1.0	null
IRF1	ENCODE Transcription Factor Targets	1.0	null
VIIIA, right, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.09763
GSE108675_2_v_1_slc1a4_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE178340_1_v_6_carfilzomib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_14128_KD_AKR1B1_SRP400403	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.64831
POLR2A_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-XOTO-3026-SM-4B65M	GTEx Tissue Sample Gene Expression Profiles	1.0	1.03079
Perturb_17640_OE_WWTR1_SRP298391	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.64668
H3K9ac_myotube_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-PWOO-0006-SM-2I3E3	GTEx Tissue Sample Gene Expression Profiles	1.0	1.07568
GSE126463_4_v_2_pomalidomide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
VMRCLCP	CCLE Cell Line Gene CNV Profiles	1.0	2.02301
Ebolavirus(ZEBOV)_7day_PBMCs_rNAPc2treated_21987740_GSE24943	GEO Signatures of Differentially Expressed Genes for Viral Infections	1.0	0.210607
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-C5-A902-01A-11R-A37O-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_astrocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K9ac_NT2-D1_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me1_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE111061_1_v_0_tofacitinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Primary visual area, layer 6b	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.27791
CTCF_GM10266_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9007_KD_ETV6_SRP273428	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.30195
regulator	GeneRIF Biological Term Annotations	1.0	null
AN3 CA	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.64772
Disease of cellular proliferation	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.687
Perturb_3963_KO_PTPN2_SRP108032	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.05563
STAT1	ENCODE Transcription Factor Targets	1.0	null
Nucleus of the lateral olfactory tract, molecular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.24155
POLR2AphosphoS5_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE248501_1_v_0_mst1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
MIXL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.2643
Perturb_18444_KD_YAP1/WWTR1/STING1_SRP303519	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.53917
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A3C8-06A-12R-A18S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_4852_KD_ZNF503_SRP059197	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.45564
Perturb_13109_KO_Foxm1_SRP194062	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-7.90742
RCOR1	ENCODE Transcription Factor Targets	1.0	null
Perturb_13727_KD_SH3PXD2AAS1_SRP330559	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
6611_PPAT_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	1.32845
ATF2_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3887_KD_EIF2B5_SRP124930	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.6264
GSE135030_3_v_0_fludarabine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-WVLH-0011-R6A-SM-3MJFZ	GTEx Tissue Sample Gene Expression Profiles	1.0	1.20334
SIN3A	ENCODE Transcription Factor Targets	1.0	null
POLR2A_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE248045,GSE248046_6_v_2_runx1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_362_KD_RAC1_SRP387923	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.09993
RUNX3_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE216273,GSE216292_14_v_3_palbociclib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_2068_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.82414
Bile duct disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.327
POLR2A_K562_hg19_6	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_HEK293_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8291_KD_RRP9_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.8414
H3K4me1_brain_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
MYC_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE147662_2_v_4_nicotinamide_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.26637
Buccal epithelial cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.834
PMC12048643-44318_2025_409_MOESM3_ESM.xlsx-regulonTargets-FOXP1_FOXP1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_3516_KD_MAGOH/MAGOHB_ERP130710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
ZNF143_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MFE-280	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
GSE228413_0_v_3_mavs_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
SNU-638	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.953968
Perturb_7812_KD_RRP40_SRP091999	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.9455
GSE235701,GSE261434_0_v_1_enasidenib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MAFK_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE224096_2_v_0_cocaine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
RCOR1-19997604-NEURONS-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
Perturb_6829_KD_CDK11_SRP156201	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.0969
liver	HPA Tissue Gene Expression Profiles	-1.0	-0.901222
BCLAF1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_631_KO_SOX4_ERP117895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.24693
GSE142210_3_v_10_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_11377_KD_TMEFF2_SRP153936	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.91037
PDE5A	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.10925
ZIM3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	36.0296
HDAC2_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-192-5p	MiRTarBase microRNA Targets	1.0	null
Perturb_11518_KD_TP63_SRP134235	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Prostate adenocarcinoma_PRAD_TCGA-CH-5751-01A-11R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE202434,GSE202438_10_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
MYC_MCF-7_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_1369_KD_GRWD1_SRP252209	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.87128
GTEX-X585-0011-R5A-SM-46MVI	GTEx Tissue Sample Gene Expression Profiles	1.0	1.00669
GSE180277_0_v_1_bach2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE218580_1_v_3_fentanyl_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
PMC12315868-Supplemental_Data_S1.xlsx-Supplemental_Data_S1F-TP53_TP53	Rummagene Transcription Factor Associations 2026	1.0	null
SNU503	CCLE Cell Line Gene CNV Profiles	1.0	1.71145
KMS-11	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.870433
KIF1A	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.42098
H3K4me3_GM12878_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE144231_3_v_5_cxcr2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE202434,GSE202438_6_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
WDR4	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.38762
Lymphatic system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.242
H3K4me3_ES-E14_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7460_KD_UPF3B_SRP120604	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.31177
Orbital area, medial part, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.80013
Perturb_11543_KD_DHX9_SRP175176	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.65293
E2F6_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H2AFZ	ENCODE Transcription Factor Targets	1.0	null
H3K4me3_LNCaP clone FGC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GATA1_G1E-ER4_mm9_8	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-P44H-0011-R1A-SM-3NM8J	GTEx Tissue Sample Gene Expression Profiles	1.0	1.42255
CW-2	COSMIC Cell Line Gene Mutation Profiles	1.0	null
6552_POLR2K_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.603149
ECPAS	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.06145
Perturb_6083_KD_UBE2I_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me3_Jurkat_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-CJ-4875-01A-01R-1305-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
SOX4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.1986
Perturb_597_OE_HOTAIR_SRP342161	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_15522_KD_AR_SRP028282	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.33461
ZMIZ1_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-CZ-5462-01A-01R-1503-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
VZ in posteroinferior (ventral) parietal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.949211
bonemarrow_6a	HPA Tissue Sample Gene Expression Profiles	1.0	1.34014
GSE150349_0_v_1_msx1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Nervous system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.641
928 MEL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.911477
Perturb_3361_OE_Bach2_SRP267100	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	6.74252
496100376_FWM_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.10082
RFX5_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
9283_TRIM59_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.582272
H3K4me2_keratinocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE146747_0_v_1_nr4a1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
SKHEP1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.41896
CTCF_osteoblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2777_KD_ZNF581_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
KDM5B	ENCODE Transcription Factor Targets	1.0	null
BARX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.705
HT-1080	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.895725
GTEX-WL46-0011-R5A-SM-3LK6V	GTEx Tissue Sample Gene Expression Profiles	1.0	1.4877
SRY	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.9643
Hypertension_Adrenal gland_GSE1674	GEO Signatures of Differentially Expressed Genes for Diseases	1.0	1.49394
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-VS-A94W-01A-12R-A37O-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
solitary nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.894839
H3K4me2_H1-hESC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_fibroblast of lung_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-CH-5761-01A-11R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_37 pcw_M_263195015	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.02823
MYCN-18555785-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
7164_RBM22_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.917889
GTEX-QVJO-0011-R2A-SM-2S1QK	GTEx Tissue Sample Gene Expression Profiles	1.0	1.4219
GTEX-XOTO-0011-R7B-SM-4B64R	GTEx Tissue Sample Gene Expression Profiles	1.0	0.954602
MKN-74	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.01272
Perturb_7563_KD_UPF1_SRP322775	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.07886
SW 1116	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.19729
LBX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.1552
Depressive Disorder	CTD Gene-Disease Associations	1.0	1.16633
znf217_22593193_mda_mb_231_gof_human_gpl570_gse35511	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.021033
7785_SEPTIN2_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.946453
MYC_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE162276_2_v_3_rosiglitazone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A51H-06A-12R-A266-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_9864_KO_MYB_SRP192629	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.98846
PMC12824661-BLOOD_BLD-2024-027020-mmc6.xls-Table_S14-HES4_Down_HES4	Rummagene Transcription Factor Associations 2026	1.0	null
Immune system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.256
GSE216273,GSE216292_0_v_8_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Right_Ventricle	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	-1.0	-1.02672
PMC9574515-mmc1.xls-THP1_0_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
paraventricular nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.20846
Perturb_12177_OE_PLK4_ERP132994	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.1864
BHLHE40_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_GM12873_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-WZTO-0011-R4A-SM-3NMC7	GTEx Tissue Sample Gene Expression Profiles	1.0	1.00569
GTEX-X4EP-0011-R2B-SM-3P625	GTEx Tissue Sample Gene Expression Profiles	1.0	0.942003
GSE65617_0_v_4_aire_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
primary visual cortex (striate cortex, area V1/17)_8 yrs_M_12981	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.25786
Perturb_8287_KD_DDX55_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.5578
Infralimbic area, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.19368
negative regulation of cell communication	GO Biological Process Annotations 2015	1.0	null
GSE210383_0_v_1_trim71_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
LNCAP-CLONE-FGC	COSMIC Cell Line Gene Mutation Profiles	1.0	null
PML	ENCODE Transcription Factor Targets	1.0	null
15361855-SuppTable1	GeneSigDB Published Gene Signatures	1.0	null
GTEX-UTHO-3026-SM-3GAFB	GTEx Tissue Sample Gene Expression Profiles	1.0	1.95715
H4K5ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Learning Disorders	CTD Gene-Disease Associations	1.0	1.53308
Perturb_535_KD_KDM1a_SRP106818	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_2358_KD_RPL7_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.22438
FOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.7578
496100409_FWM_no dementia_TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.09397
REST_HL-60_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE239844_8_v_10_crizotinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
inner SZ in midlateral temporal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.99011
Endocrine gland cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.716
ELF1	ENCODE Transcription Factor Targets	1.0	null
FOXO1::ELK1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.0205
H3K27ac_HCT116_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_14160_KD_IPO11_SRP316321	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.83888
USF1_A549_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_12108_KD_CCND1_SRP244245	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE207978_1_v_0_rai1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
periventricular stratum of r7Co	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.13451
PMC6080909-JEM_20171312_TableS1.xlsx-Each_THP1_Pulldown_Expt_Targets-Unnamed_1_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
NRF1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2771_KD_IRX6_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Ranolazine_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0163814
GTEX-WHSE-0011-R2A-SM-3P5ZL	GTEx Tissue Sample Gene Expression Profiles	1.0	1.79883
POLR2A_GM18505_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC11502753-41467_2024_53330_MOESM11_ESM.xlsx-Sheet1-DREAM_target_genes_KCNIP3	Rummagene Transcription Factor Associations 2026	1.0	null
GSE102598_1_v_2_nmda_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
GSE148200_4_v_2_gemcitabine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
BICR18	CCLE Cell Line Gene CNV Profiles	1.0	2.04592
H2BK20ac_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
membrane-bounded organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
GSE65617_0_v_1_aire_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_8158_KD_HNRNPLL_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.4306
VZ in midlateral temporal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.82483
Perturb_12379_KO_SMARCA4_SRP324802	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.93671
GSE162087_0_v_1_dexamethasone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_11427_OE_FOSL1_SRP360169	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_9032_KD_FOSL1/FOSL2_SRP320789	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.1184
MYC_MCF-7_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-RVPU-0011-R7A-SM-2XCAB	GTEx Tissue Sample Gene Expression Profiles	1.0	0.874321
Cholangiocarcinoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.927
Perturb_15514_KD_E2F1_SRP314859	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.75019
Perturb_14891_KO_H15_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.72252
GSE202434,GSE202438_2_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
NCIH2291	CCLE Cell Line Gene Expression Profiles	1.0	1.94281
periventricular stratum of Dg	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.28742
Stomach cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.83
Perturb_463_KO_IGF2BP1_SRP251874	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.3113
NCI-H2110	COSMIC Cell Line Gene Mutation Profiles	1.0	null
H3K4me2_HepG2_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-NL4W-0011-R11A-SM-2I3DW	GTEx Tissue Sample Gene Expression Profiles	1.0	1.16283
FOXL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	37.862
Perturb_10059_KD_XRN2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.82761
Perturb_1139_KO_Ahr_ERP113014	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	2.39306
GSE149903_4_v_2_myd88_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CTCF_fibroblast of pulmonary artery_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MAX_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
E2F6_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8190_KD_HNRNPU_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.87837
Immune system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.368
3054_FECH_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.519126
TBP_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
18787207-TableS2	GeneSigDB Published Gene Signatures	1.0	null
Perturb_14853_KD_TEAD4_SRP247403	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.59135
Perturb_15442_KD_MED25_SRP212208	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.34163
H3K4me3_endothelial cell of umbilical vein_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
LCLC-97TM1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.832028
GTEX-OIZG-0526-SM-2HMLF	GTEx Tissue Sample Gene Expression Profiles	1.0	0.960588
Perturb_2063_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.37655
GSE245134_2_v_3_atg5_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Renal Cell Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
6708_PPWD1_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.693886
GSE135352_0_v_4_napabucasin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_8302_KD_RBM22_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.3773
PMC10251551-12885_2023_11010_MOESM4_ESM.pdf-38-ENSG00000196458_ZNF605	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me2_fibroblast of lung_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
non-Hodgkin lymphoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.005
Tumor Cell Invasion	DisGeNET Gene-Phenotype Associations	1.0	null
caudal portion of VFC (area 44)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.859368
hsa-miR-4786-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.843347
H3K4me3_Adipose Nuclei	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Connective tissue cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.0
Perturb_8093_KD_PUM1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
TAF1_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-QDVJ-1926-SM-2S1PJ	GTEx Tissue Sample Gene Expression Profiles	1.0	0.970689
hsa-miR-1251	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.40969
Perturb_8134_KD_FXR1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.43404
SPI1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2336_KD_WBP11_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.09544
Fibrosis	CTD Gene-Disease Associations	1.0	1.31897
Perturb_14378_KD_PAX8_SRP276625	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.80314
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-7_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
SNU-216	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.989333
H3K4me3_fibroblast of lung_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8789_Mut_HNF6_SRP217514	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.455
Perturb_11387_OE_OC2_SRP122890	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.06602
b16f0	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.553
PMC7371429-elife-53600-supp2.xlsx-annotated_MEIS1_in_B13ko-M1-Gene_Name_MEIS1	Rummagene Transcription Factor Associations 2026	1.0	null
SWSAP1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.27932
outer SZ in dorsomedial extrastriate cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.54274
5900_NUP62_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.560309
Perturb_15185_KD_CPSF1_SRP186931	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.50493
496100616_FWM_no dementia_TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.6225
intermediate stratum of OB	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.02871
H3K4me3_fibroblast of the aortic adventitia_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
HOXC13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.4782
GTEX-WHSE-0011-R4A-SM-3P5ZN	GTEx Tissue Sample Gene Expression Profiles	1.0	1.25824
Perturb_6750_KO|KD_IER5_SRP103746	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.24646
GSE223008_7_v_8_calhm6_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
496100317_FWM_no dementia_no TBI_81_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.83061
Perturb_13902_KO_AS3MT_SRP332674	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.39637
H2AFZ_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.75177
GSE148200_1_v_2_gemcitabine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K4me3_liver_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
UBTF_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HCC3153	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	1.76524
amygdaloid complex_4 mos_M_12296	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.80343
Perturb_8762_KD_TP53_SRP161806	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GTEX-WWYW-0011-R11A-SM-3NB38	GTEx Tissue Sample Gene Expression Profiles	1.0	1.10953
Nasopharyngeal disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.143
Perturb_14203_KD_ERBB2_ERP118856	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
BGC-823 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.855
GSE89018_6_v_14_cry2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_14177_KO_CD33_SRP387539	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
HDAC2_MCF-7_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-X4XX-0011-R4B-SM-46MWL	GTEx Tissue Sample Gene Expression Profiles	1.0	1.0502
CTBP2	ENCODE Transcription Factor Targets	1.0	null
Perturb_6068_KD_SAFB2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Orbital area, ventrolateral part, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.1245
Perturb_7172_KD_FTH1_SRP385887	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.44175
whole body	TISSUES Experimental Tissue Protein Expression Evidence Scores	1.0	0.23362
H3K9ac_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
protein binding	GO Molecular Function Annotations 2015	1.0	null
Perturb_2460_KD_TET2_SRP268806	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.63056
GSE214596,GSE214598_1_v_3_rosiglitazone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Retrosplenial area, ventral part, layer 6b	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.79407
TCF12_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE203308_6_v_3_brf1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
posterior triangular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.22953
USF1_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
KAT2A	ENCODE Transcription Factor Targets	1.0	null
GSE198165,GSE198166_6_v_3_zfp266_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
POLR2AphosphoS2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_13940_KD_SETD8_SRP075406	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.69334
SIN3A_H1-hESC_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-Q2AG-0426-SM-2S1PU	GTEx Tissue Sample Gene Expression Profiles	1.0	2.01242
Lung adenocarcinoma_LUAD_TCGA-62-A46O-01A-11R-A24H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_7298_KD_PCIF1_SRP162223	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	12.5322
A_CA_04_2009_4dayMOI-10^4_None_GSE37569	GEO Signatures of Differentially Expressed Genes for Viral Infections	1.0	1.34066
VZ in dorsomedial extrastriate cortex (V2)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.12542
Perturb_8764_KD_SLIT2_SRP158939	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.59949
GSE202434,GSE202438_8_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_12138_KD_OTX2_SRP347033	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.53405
GTEX-RVPV-0011-R5A-SM-2TF69	GTEx Tissue Sample Gene Expression Profiles	1.0	1.42105
20418243-SuppTable1c	GeneSigDB Published Gene Signatures	1.0	null
NRF1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8260_KD_RPLP0_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
orbital frontal cortex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.10924
Psoas_Muscle	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	-1.0	-1.66012
Perturb_3655_KO_MTHFD1_SRP120974	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Kidney renal papillary cell carcinoma_KIRP_TCGA-F9-A7Q0-01A-11R-A36F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Pharyngeal cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.012
BRCA1_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GC-1 spg cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.997
anterior olfactory area, dorsal part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07354
CTCF_A549_hg19_7	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6490_KD_NONO_SRP350991	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.48277
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	2.65201
Organ system cancer	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
GSE181966_5_v_3_has2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
brain	GTEx Tissue Gene Expression Profiles	1.0	2.18987
pancreas	GTEx Tissue Gene Expression Profiles	-1.0	-1.00799
Brain Lower Grade Glioma_LGG_TCGA-DB-5276-01A-01R-1470-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
MSX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.4335
OSC19	DepMap CRISPR Gene Dependency	1.0	7.52579
GSE202434,GSE202438_8_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
tardbp_19910924_hek293e_lof_human_gpl570_gds3730	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.166811
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.74518
GTEX-WVLH-3026-SM-3MJG9	GTEx Tissue Sample Gene Expression Profiles	1.0	0.945692
deep layers of caudal entorhinal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.881574
thymus	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	1.0	1.15885
KIF23	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.40654
Perturb_2764_KD_FOXA1_SRP077334	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
CTCF_keratinocyte_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
BCLAF1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
inner SZ in posterior parahippocampal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.32261
H3K4me1_Panc1_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Lateral visual area, layer 6b	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.40188
KAT2A_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K9me3_Breast Myoepithelial Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE211215_1_v_0_pemetrexed_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE132369,GSE132371_4_v_0_cccp_human	RummaGEO Drug Perturbation Signatures	-1.0	null
posteromedial visual area, layer 6b	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.46965
anteroventral periventricular preoptic nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.18418
GSE143944_1_v_0_ribociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
CHD1_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.88992
Lung squamous cell carcinoma_LUSC_TCGA-63-A5MJ-01A-11R-A27Q-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
corpus callosum	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	2.1023
CTCF_CD14-positive monocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE119978,GSE180930_6_v_7_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE137144_3_v_1_nlrp3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GTEX-NPJ8-0011-R3a-SM-2HMIW	GTEx Tissue Sample Gene Expression Profiles	1.0	0.974159
Bed nuclei of the stria terminalis, anterior division, juxtacapsular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.85485
POLR2AphosphoS5_GM12892_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HDAC6_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PAX5_GM12878_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CEBPB_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
substantia innominata/basal nucleus, transitional part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.39212
GSE199255,GSE199356_6_v_1_pds5a_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NUGC-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
A253	CCLE Cell Line Gene Expression Profiles	1.0	2.19314
CTCF_K562_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Ubiquitin conjugating enzyme complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.912
Perturb_8266_KD_EIF3D_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.29432
POLR2A_GM15510_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE70935_3_v_5_cyfip1_human	RummaGEO Gene Perturbation Signatures	1.0	null
NCI-H292 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.585
Perturb_15531_KD_YAP1/WWTR1_SRP360171	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.28975
GSE158715_2_v_4_cyp1b1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
E2F1	ChEA Transcription Factor Targets	1.0	null
MYC_MCF 10A_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9667_KO_NR1H4_SRP115904	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.69168
arcuate nucleus of hypothalamus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.857609
PMC8755726-42003_2021_2958_MOESM6_ESM.xlsx-489_corr_genes_TWIST1_signature-Gene_name_TWIST1	Rummagene Transcription Factor Associations 2026	1.0	null
gigantocellular group, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.955393
Urogenital Abnormalities	CTD Gene-Disease Associations	1.0	1.37217
GSE111247_2_v_13_temozolomide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE149943_1_v_3_cd8a_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Sec61 translocon complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.149
GSE153189_1_v_0_interferon gamma_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_15110_KD_PPHLN1_SRP218207	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.18614
GTEX-Q2AG-0011-R2A-SM-2HMIT	GTEx Tissue Sample Gene Expression Profiles	1.0	1.86
POLR2A_MCF-7_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-B0-5084-01A-01R-1334-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
MFM223	DepMap CRISPR Gene Dependency	1.0	2.25271
THAP1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MEPCE	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.82335
NCOR1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K9me3_fibroblast of lung_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-P44H-0011-R4A-SM-2XCEW	GTEx Tissue Sample Gene Expression Profiles	1.0	1.04024
POLR2A_small intestine_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TFAP4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	43.4409
TCF7L2_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC10363146-41598_2023_38681_MOESM1_ESM.pdf-500-EBF3_EBF3	Rummagene Transcription Factor Associations 2026	1.0	null
CTCF_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
V, left, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.986029
Bladder Urothelial Carcinoma_BLCA_TCGA-FD-A3SP-01A-31R-A22U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Primary somatosensory area, lower limb, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.017
Secondary motor area, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-4.10569
MAX_HCT116_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXO4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.301
OCT4-20526341-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
CTCF_astrocyte of the cerebellum_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
primary auditory cortex (core)_1 yrs_F_12830	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.06615
GTEX-T5JC-2426-SM-3NMDB	GTEx Tissue Sample Gene Expression Profiles	1.0	0.952319
GSE233049_1_v_3_atf3_human	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_14611_KO_MTAP_SRP186070	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.43375
High grade glioma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.438
Perturb_2088_OE_APTX_SRP174572	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
an3ca	HPA Cell Line Gene Expression Profiles	-1.0	-0.978557
Liver Neoplasms	CTD Gene-Disease Associations	1.0	1.12323
HOXB13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.3719
CTCF_astrocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE100316_5_v_6_mtor_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
B4GALT6	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.34355
CREM-20920259-GC1-SPG-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
intermediate stratum of p2Lim	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.00722
GTEX-XBEW-0226-SM-4AT6A	GTEx Tissue Sample Gene Expression Profiles	1.0	0.882864
6652_PPP1R10_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.549813
Perturb_11857_KO_miR301a_SRP131007	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	2.95559
NAP1L3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.28018
17009876-tableS1b	GeneSigDB Published Gene Signatures	1.0	null
FOXM1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MAX_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
rituximab_homo sapiens_gpl570_gds3829	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
JUN	ENCODE Transcription Factor Targets	1.0	null
HDQP1	CCLE Cell Line Gene CNV Profiles	1.0	1.66977
Perturb_8303_KD_SRFBP1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.5996
GSE162276_5_v_3_rosiglitazone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
SCC-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.08286
Perturb_12160_OE_TCF7_SRP144189	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.30457
HOXC9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.9246
Melanoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.33
BACH1	ENCODE Transcription Factor Targets	1.0	null
MYC	ENCODE Transcription Factor Targets	1.0	null
Prelimbic area, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.66801
H3K4me3_K562_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
KDM5A	ENCODE Transcription Factor Targets	1.0	null
NRF1	Pathway Commons Protein-Protein Interactions	1.0	null
Perturb_8050_KD_METTl14_SRP167173	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.39907
Perturb_8166_KD_CNOT7_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.49606
GSE151090_0_v_1_verteporfin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MAX_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15796_KD_EMP2_SRP265560	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-15.6283
primary somatosensory cortex (area S1, areas 3,1,2)_13 yrs_F_12831	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.928017
H3K4me1_cortical plate_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K27ac_cerebellum_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_BE2C_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF667	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.42619
MAP3K1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.73482
CTCF_fibroblast of pedal digit skin_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC4165364-13059_2014_406_MOESM5_ESM.xls-Supp_Dataset_1-SUPPLEMENTARY_DATASET_1_AML3_AzaC_SigDiff_1147_Note_to_reviewers_-_view_these_files_as_xls_RUNX2	Rummagene Transcription Factor Associations 2026	1.0	null
GSE184087_4_v_1_tert_human	RummaGEO Gene Perturbation Signatures	1.0	null
MAX	ENCODE Transcription Factor Targets	1.0	null
FOXH1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.3799
Retrosplenial area, dorsal part, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.52824
Posterolateral visual area, layer 6a	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.34927
Perturb_9964_KD_NSUN2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.28563
Perturb_2095_KD_EIF4A3_SRP226707	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.99057
H3K27ac_myotube_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
MYC-19030024-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
Prostate Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
PMC3607232-mmc3.xlsx-a_RUNX1_SEM_MLLN_AF4C_H3K79Me-x_RUNX1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_14388_KD_PAX8_SRP276625	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.74863
H2AFZ_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2A_GM12878_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
biological_process	GO Biological Process Annotations 2015	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-EE-A2MC-06A-12R-A18S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_6520_KD_HES3_SRP162877	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.72192
GSE153189_1_v_0_stat1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
amygdaloid complex_12 pcw_F_12960	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.874586
GSE206870,GSE206872_1_v_5_ascl1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H2AFZ_osteoblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14900_KO_H15_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.06409
E2F6_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_13948_KD_CDK4/CDK6_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.72266
GSE98898_8_v_1_hoxa1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
ICC10	DepMap CRISPR Gene Dependency	1.0	2.66479
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-A499-01A-11R-A24H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Hematopoietic system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.358
GSE157555,GSE157556_3_v_7_foxa2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE207728,GSE207808_2_v_1_c646_human	RummaGEO Drug Perturbation Signatures	-1.0	null
YY1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MYC_MCF 10A_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
caco2	HPA Cell Line Gene Expression Profiles	-1.0	-1.09749
Perturb_11528_KD_ATAC1_SRP109127	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Peripheral nervous system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.134
Perturb_3885_KD_EIF2B5_SRP124930	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.32691
A-Vietnam-1203-2004(H5N1)_24Hour_21865398_GSE28166	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.92278
Perturb_9970_KD_WDR43_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.47471
POLR2A_Raji_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE227415_1_v_0_ucp1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_7231_KD_UPF1LL_SRP295982	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.29164
INSYN1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.52725
Perturb_531_KD_NKX22_SRP234742	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.15772
Perturb_8113_KD_U2AF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.6346
Perturb_9968_KD_UPF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.24139
YY1_GM12892_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2AphosphoS5_HepG2_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Pallidum, caudal region	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.23601
Myeloid leukemia	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.17
inner portion of lateral ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.20552
Perturb_16504_KD_NKX21/PROX1/ASCL1_SRP262644	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.94345
Goserelin (acetate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0166188
COLO-818	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.837378
WiDr cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.636
Perturb_5653_KD_EWSR1_SRP117628	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.71723
VZ in orbital frontal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.24276
YY1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Nasopharyngeal carcinoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.847
Nasopharynx carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.162
KDM1A_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2466_KD_NDP52_SRP345458	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.56253
GSE188870,GSE188871_4_v_2_kat7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GTF2F1	ENCODE Transcription Factor Targets	1.0	null
layer 1 of FCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.36985
Perturb_625_KD_IGF2BP3_SRP068523	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.01004
GSE85302_4_v_1_kat6a_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Fetal Brain	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE201042_2_v_4_ptpmt1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_endothelial cell of umbilical vein_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
NFATC1	ENCODE Transcription Factor Targets	1.0	null
PMC4165364-13059_2014_406_MOESM5_ESM.xls-Supp_Dataset_3-SUPPLEMENTARY_DATASET_3_AML3_AzaC_WIMSi_246_RUNX2	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_2073_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.65201
SK-MEL-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.832953
H3K4me1_Colon Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
DB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.75857
GSE77108_8_v_1_saha_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_14761_KD_LATS1/LATS2_SRP345234	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.0237
GSE146253_0_v_2_stat4_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Kidney renal papillary cell carcinoma_KIRP_TCGA-BQ-5893-01A-11R-1592-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE153836_11_v_2_fluoxetine_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-QVUS-2826-SM-3GADB	GTEx Tissue Sample Gene Expression Profiles	1.0	1.90601
RCOR1	ChEA Transcription Factor Targets	1.0	null
SARS-BatSRBD_Day7_None_GSE50000	GEO Signatures of Differentially Expressed Genes for Viral Infections	1.0	1.55313
Perturb_8223_KD_CKAP4_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
hsa-miR-4418	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.13535
periventricular stratum of SeStr	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.29247
occipital pole, left, inferior aspect	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.37562
POLR2A_GM12878_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE231648_0_v_2_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE94849_7_v_4_pinometostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE203308_14_v_3_brf1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE158834_7_v_8_palmitic acid_human	RummaGEO Drug Perturbation Signatures	1.0	null
Frontal pole, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.06733
GSE216273,GSE216292_0_v_3_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
hsa-miR-875-3p	TargetScan Predicted Conserved microRNA Targets	1.0	0.075559
NANOG-19829295-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
GSE193541_0_v_3_nifurtimox_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-XLM4-0011-R4B-SM-4AT5C	GTEx Tissue Sample Gene Expression Profiles	1.0	0.996448
HCC2270	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.26146
ccnd1_18413728_imr_neuroblastoma_lof_human_gpl570_gse8866	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.585419
Annulate lamellae	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.99
H3K4me1_CH12.LX_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
SARS-CoV MA15_Day7-CXCR3KO_None_GSE50878	GEO Signatures of Differentially Expressed Genes for Viral Infections	1.0	1.20687
Perturb_15102_KD_SREBF2_SRP385600	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.58837
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00206
IPC298	CCLE Cell Line Gene CNV Profiles	-1.0	-2.00076
H3K4me3_mononuclear cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
nb4	HPA Cell Line Gene Expression Profiles	-1.0	-1.0617
Perturb_9084_KO_NSUN2_SRP400807	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	12.4896
GATA3	ENCODE Transcription Factor Targets	1.0	null
Anethole trithione_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0313003
PA-TU-8902	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.849058
MEF2C	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	55.6953
E2F1	JASPAR Predicted Transcription Factor Targets	1.0	null
Perturb_8798_OE_HOTAIR_SRP352837	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.23464
Perturb_9311_KD_Trp53_SRP320074	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.51776
FOXC1	JASPAR Predicted Transcription Factor Targets	1.0	null
Perturb_11562_KD_BAX/BAK_SRP348085	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_7763_KD_IER3_SRP348787	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.12411
Perturb_13599_KO_HDGFL2_SRP153901	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.17579
Hepatobiliary system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.765
496100554_FWM_no dementia_no TBI_78_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.08663
SF3A1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.12632
non-small cell lung cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.605
GSE223908,GSE223909_4_v_8_serpinb3_human	RummaGEO Gene Perturbation Signatures	-1.0	null
vagina	HPA Tissue Protein Expression Profiles	-1.0	-1.44043
gata3_22922362_treg_cd4poscd25posyfppos_lof_mouse_gpl8321_gse39864	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.491442
Primary Malignant Neoplasm Of Lung	DisGeNET Gene-Disease Associations	1.0	null
GTEX-VJWN-0426-SM-3GIJI	GTEx Tissue Sample Gene Expression Profiles	1.0	1.15299
Perturb_6443_KO_YAP_SRP134183	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.38761
Perturb_309_KD_YTHDF1_SRP256259	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.9765
inner SZ in dorsomedial frontal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.964635
Kidney renal clear cell carcinoma_KIRC_TCGA-A3-3385-01A-02R-1420-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_15109_KD_MPP8_SRP218207	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.4505
MXI1_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_astrocyte of the cerebellum_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-QK-A6V9-01A-11R-A34R-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC5404927-elife-24463-supp1.xlsx-1b_ERM_proteome-Gene_names_ETV5	Rummagene Transcription Factor Associations 2026	1.0	null
Postsubiculum, layer 3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.67913
HMGN3	ENCODE Transcription Factor Targets	1.0	null
hippocampus (hippocampal formation)_16 pcw_M_12879	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.19412
Connective tissue disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.186
Bladder Urothelial Carcinoma_BLCA_TCGA-E7-A5KE-01A-11R-A28M-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
brain_3c	HPA Tissue Sample Gene Expression Profiles	1.0	1.11158
Perturb_14324_KD_EIF5A2_SRP294329	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Primary somatosensory area, trunk, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.0891
Head and Neck squamous cell carcinoma_HNSC_TCGA-BA-5153-01A-01R-1436-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE142210_2_v_10_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
outer SZ in lateral temporal-occipital cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.828713
homolog	GeneRIF Biological Term Annotations	1.0	null
Perturb_14599_KD_IGF2BP1_SRP252427	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.23692
CTCF_GM12874_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SOX2-19829295-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
PPP1R1A_KO_GDS1920_708_mouse_hippocampus	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
Perturb_679_KO_CX_SRP212091	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.55285
TEAD4_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9158_KD_RNF213_SRP345502	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.49131
GSE216273,GSE216292_0_v_7_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MEF2A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	65.8749
ntera2	HPA Cell Line Gene Expression Profiles	1.0	1.60903
RNF2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF384_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_myotube_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
SIN3A_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-NL4W-0011-R4a-SM-2I5GZ	GTEx Tissue Sample Gene Expression Profiles	1.0	1.15279
Head and Neck squamous cell carcinoma_HNSC_TCGA-CV-7261-01A-11R-2016-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GTEX-N7MS-0011-R5a-SM-2HMK8	GTEx Tissue Sample Gene Expression Profiles	1.0	1.60381
GTEX-QVUS-0011-R1A-SM-3GAD2	GTEx Tissue Sample Gene Expression Profiles	1.0	1.58265
CTCF_fibroblast of lung_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
RCOR1_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE111247_11_v_3_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_3591_KO_DDX6_ERP024006	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.3465
FOXB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	46.7095
GSE255680_2_v_0_igf2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	41.4907
NFYB_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_11580_KD_BUD23_ERP119404	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.31155
GSE67266_5_v_1_etoposide_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
immune	GeneRIF Biological Term Annotations	1.0	null
Perturb_9861_KO_MYB_SRP192629	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.68528
Kidney renal clear cell carcinoma_KIRC_TCGA-B0-4688-01A-01R-1277-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
amygdaloid complex_12 pcw_F_12835	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.31307
H3K9me3_Colonic Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE88819_7_v_8_tug1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
496100514_FWM_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.21121
TAF1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FARAGE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.897569
hsa-miR-3128	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.13535
GSE228894_0_v_2_rnmt_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-FD-A3SN-01A-12R-A22U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2077_KD_PUM2_SRP072710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.15044
POLR2A_GM12891_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-XOTO-0011-R5A-SM-4B657	GTEx Tissue Sample Gene Expression Profiles	1.0	1.05016
GSE147210_3_v_5_kmt2d_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE77178_5_v_3_ccnd1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GTEX-NPJ8-0011-R5a-SM-2HMJY	GTEx Tissue Sample Gene Expression Profiles	1.0	1.02954
8666_TAF5_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.52475
GSE202434,GSE202438_7_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
amygdaloid complex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.50888
FOXM1-23109430-U2OS-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
Perturb_14841_KD_GCM1_SRP358680	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.2815
HCFC1_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
inner SZ in medial temporal-occipital cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.79267
absent extraembryonic ectoderm	MGI Mouse Phenotype Associations 2023	1.0	null
ubiquitin-protein transferase activity	GO Molecular Function Annotations 2025	1.0	null
GSE254155_1_v_0_per2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Pancreatic adenocarcinoma_PAAD_TCGA-F2-6879-01A-11R-2156-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me1_CH12.LX_mm9_4	ENCODE Histone Modification Site Profiles	1.0	null
layer 4 of FCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.19286
Bladder Urothelial Carcinoma_BLCA_TCGA-C4-A0F1-01A-11R-A034-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me1_Colonic Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE143994_0_v_1_ythdf1_human	RummaGEO Gene Perturbation Signatures	1.0	null
periventricular stratum of r6Co	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07214
Lung squamous cell carcinoma_LUSC_TCGA-51-4080-01A-01R-1100-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
POLR2A_HepG2_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HDAC2_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TBP_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8803_KD_HOTAIR_SRP352837	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.3186
OCIM1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.69238
Perturb_14561_KD_UBE2C_SRP221206	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE111247_2_v_8_temozolomide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_9152_KD_DDX21_SRP327839	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.6091
Anteroventral preoptic nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.21072
SAP30_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Melanoma	DisGeNET Gene-Disease Associations	1.0	null
GATA1_G1E-ER4_mm9_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
lateral ganglionic eminence_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.48461
Perturb_2563_OE_GATA3|JUN_SRP188712	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-18.5376
LNCAP	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	1.0	null
CiliaryGanglion	BioGPS Human Cell Type and Tissue Gene Expression Profiles	1.0	1.02798
Perturb_6021_KD_HNRNPA2B1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
reticulotegmental nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.976902
Inflammation	CTD Gene-Disease Associations	1.0	1.46225
ZNF677	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	51.575
Demeclocycline_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0370296
Kidney renal clear cell carcinoma_KIRC_TCGA-CZ-4861-01A-01R-1305-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
vitamin c_homo sapiens_gpl570_gds3635	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
GTEX-NPJ7-2826-SM-2I3FU	GTEx Tissue Sample Gene Expression Profiles	1.0	0.920338
Perturb_2419_KD_DDX3X_ERP105312	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.67899
Nasopharyngeal carcinoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.965
Perturb_6087_KD_XRN2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.40736
CAMA1	DepMap CRISPR Gene Dependency	1.0	4.25503
H3K36me3_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC5640240-ppat.1006668.s013.xlsx-MAX_ChIP_shEP400-1-Unnamed_6_MAX	Rummagene Transcription Factor Associations 2026	1.0	null
NTERA-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.11251
GSE128730_7_v_6_neratinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE189609_1_v_2_hax1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
arcuate nucleus of the hypothalamus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.940411
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00091
Brain Lower Grade Glioma_LGG_TCGA-HT-7481-01A-11R-2027-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
ZNF143	ENCODE Transcription Factor Targets	1.0	null
GSE100316_0_v_6_mtor_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE160817_7_v_9_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
negative regulation of intracellular signal transduction	GO Biological Process Annotations 2023	1.0	null
H3K4me3_bronchial epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Ubiquitin activating enzyme complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.198
POLR2A_MEL cell line_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
LDHB	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.08685
pancreas	HPA Tissue Protein Expression Profiles	1.0	1.24946
GSE216043_11_v_9_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-EE-A29M-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
trim59	GeneRIF Biological Term Annotations	1.0	null
GSE264621_1_v_6_secretin_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE217363_4_v_1_nlrp3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE149264,GSE149267_9_v_3_trp53_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
ELK1	ENCODE Transcription Factor Targets	1.0	null
Perturb_9972_KD_BCLAF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.65766
POLR2AphosphoS5_HCT116_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9092_KD_HUR_SRP293260	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.53006
Kidney renal papillary cell carcinoma_KIRP_TCGA-B3-3926-01A-02R-1351-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
posterior (caudal) superior temporal cortex (area 22c)_10 mos_M_12977	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.06737
H4K20me1_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE110708_2_v_3_adar_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Hepatobiliary disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.678
MYC_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE145915_5_v_1_pcm1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_4592_KD_EBNA1_SRP064652	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.73462
H3K4me1_Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE242290_1_v_2_glutathione_human	RummaGEO Drug Perturbation Signatures	-1.0	null
hsa-miR-103a	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
GSE134375_3_v_2_stat3_human	RummaGEO Gene Perturbation Signatures	1.0	null
MYOG_myocyte_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
A-CA-04-2009(H1N1)_3Hour_None_GSE37571	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.09975
RFX5_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HOXB9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3042
A-CA-04-2009(H1N1)_48Hour_23935999_GSE47961	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.516
BICR22	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
GTEX-NPJ8-0011-R11A-SM-2YUMS	GTEx Tissue Sample Gene Expression Profiles	1.0	1.20517
LRIG2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.0175
intermediate stratum of RtC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.04958
USF2	JASPAR Predicted Transcription Factor Targets	1.0	null
Perturb_3530_KD_circCDKN2BAS1_SRP252917	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
KU812	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00091
Prostate disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.705
STAT1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27ac_GM12878_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
Perturb_7508_OE_ILF2_SRP195616	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.51365
cellular_component	GO Cellular Component Annotations 2015	1.0	null
ubiquitin-protein transferase activity	GO Molecular Function Annotations 2023	1.0	null
Perturb_85_KD_CSN5_SRP316687	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.5546
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44043
OVCAR-5	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.08932
FOXM1-23109430-U2OS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
PMC8528285-pbio.3001085.s010.xlsx-Fig_7E-MLX_TESTES_MLX	Rummagene Transcription Factor Associations 2026	1.0	null
SP in caudal midinferior temporal cortex (area TF)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.890536
H3K4me3_MEL cell line_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_MCF-7_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-TSE9-0011-R7A-SM-3DB7P	GTEx Tissue Sample Gene Expression Profiles	1.0	1.06604
GSE188870,GSE188871_4_v_5_kat7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Lumateperone (tosylate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0162592
inner SZ in superolateral temporal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.34018
A_CA_04_2009_7dayMOI-10^5_None_GSE37569	GEO Signatures of Differentially Expressed Genes for Viral Infections	1.0	1.69732
H3K4me1_mononuclear cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-QDT8-0011-R7A-SM-32PKF	GTEx Tissue Sample Gene Expression Profiles	1.0	0.836425
HT-144	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1236
GSE195568_1_v_7_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
ELK1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE142210_2_v_7_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE192663_3_v_2_acly_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE216273,GSE216292_0_v_2_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE215086_8_v_7_batf_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K27ac_MCF-7_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-X4XY-0626-SM-4E3IN	GTEx Tissue Sample Gene Expression Profiles	1.0	0.987071
PMC12254391-41598_2025_8960_MOESM5_ESM.xlsx-Suppl_Table_6_DEG-Supplemental_Table_6_Differentially_Expressed_Genes_DEG_between_siRNA_DLX4_and_siRNA_control_n_3_RA_FLS_cell_lines_per_treatment_group_DLX4	Rummagene Transcription Factor Associations 2026	1.0	null
layer 6a of PaS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.93013
Lung squamous cell carcinoma_LUSC_TCGA-60-2726-01A-01R-0851-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
prostate	HPA Tissue Protein Expression Profiles	1.0	1.24946
GTEX-WWYW-0011-R8A-SM-3NB3S	GTEx Tissue Sample Gene Expression Profiles	1.0	1.12145
TP53	Pathway Commons Protein-Protein Interactions	1.0	null
GSE242199_6_v_7_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Malaria	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.852288
PMC7782476-41467_2020_20434_MOESM7_ESM.xlsx-KLF14_string_interactions-node1_KLF14	Rummagene Transcription Factor Associations 2026	1.0	null
LRIG1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.78473
layer 1 of AOV cortex	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.37873
Bladder Urothelial Carcinoma_BLCA_TCGA-FD-A43P-01A-31R-A23W-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE158456_2_v_3_furin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC12500496-262_2025_4178_MOESM2_ESM.xlsx-THP1_enriched_for_control-gene_name_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
GSE122067_2_v_1_mtch2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
ets_00000000_2008_ovarian_cancer_cells_gof_human_gpl6244_gse21129	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.092853
PHOX2B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	44.5569
Perturb_11410_KD_MYC_SRP218384	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.15054
Perturb_427_KD_FOXM1_SRP371675	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.26621
GSE122215,GSE122217_5_v_2_peg10_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_3660_KO_ZCCHC4_SRP189763	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.51981
POLR2A_GM10847_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SOX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4118
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.976343
Perturb_11534_KD_THOR_SRP121007	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.3372
Arcuate hypothalamic nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.90665
Perturb_6086_KD_XRN2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.36781
PMC6855629-pone.0225186.s008.xlsx-Sheet1-DEGs_upregulated_in_SK-N-SH_MEIS1_OE_MEIS1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_7168_KD_ACTG1_SRP385887	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.56875
KAT2A_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2354_KD_FOXQ1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	17.4437
posterior tegmental nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.62433
Stomach Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
DMS79	CCLE Cell Line Gene Expression Profiles	-1.0	-1.46231
EBF1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
skmel30	HPA Cell Line Gene Expression Profiles	-1.0	-2.20704
GTEX-PVOW-0011-R5A-SM-32PL7	GTEx Tissue Sample Gene Expression Profiles	1.0	1.98331
Perturb_3910_KO_ARID1A_ERP114370	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.366
MAX_MCF-7_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXK1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.8902
NCM-460 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.831
POLR2A_lung_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2090_KD_H2AZ1_SRP199103	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.03403
GSE169152_3_v_2_ibrutinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MYC-18358816-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
superior olivary complex, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.898203
Perturb_9185_OE_ZNF593AS_SRP298754	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_13604_KD_YAP1/WWTR1_SRP221804	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	14.9094
POLR2A_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-509-3-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
GTEX-N7MT-0011-R4a-SM-2I3G9	GTEx Tissue Sample Gene Expression Profiles	1.0	1.21386
HEL9217	DepMap CRISPR Gene Dependency	1.0	3.74615
Lateral visual area, layer 6a	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.00581
Pancreatic ductal adenocarcinoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.678
CTCF_GM12874_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-XLM4-0011-R9A-SM-4AT45	GTEx Tissue Sample Gene Expression Profiles	1.0	0.826517
VI	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.06409
H3K4me1_osteoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
gata3_21892208_mda_mb_231_gof_human_gpl570_gds4080	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.340641
GTEX-WWYW-0011-R10A-SM-3NB35	GTEx Tissue Sample Gene Expression Profiles	1.0	1.53814
Perturb_3750_KD_NORAD_SRP149071	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.83426
CTCF	ENCODE Transcription Factor Targets	1.0	null
POLR2A_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE193402_0_v_2_imatinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
ICC3	DepMap CRISPR Gene Dependency	1.0	2.55548
OCI-AML2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.30962
Perturb_14051_OE_NFIB_SRP281947	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.4314
GSE140576_0_v_2_plag1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE214596,GSE214598_1_v_2_rosiglitazone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
CTCF_GM12865_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE169152_5_v_4_ibrutinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_8928_KD_CHD4_SRP350011	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.8969
HCC1143	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.36934
Perturb_2803_KO_CDH1_SRP267080	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.06135
MTA3	ENCODE Transcription Factor Targets	1.0	null
Perturb_15160_KD_MTOR_SRP192607	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.65237
SP1	ENCODE Transcription Factor Targets	1.0	null
PBX3	ENCODE Transcription Factor Targets	1.0	null
MXI1_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K9ac_A549_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE135514_2_v_0_dasatinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
SPI1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-T6MN-2526-SM-32PMN	GTEx Tissue Sample Gene Expression Profiles	1.0	1.04739
integral component of membrane	GO Cellular Component Annotations 2015	1.0	null
TYK-NU	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.36299
Carcinoma, Ovarian Epithelial	DisGeNET Gene-Disease Associations	1.0	null
GSE190681_1_v_0_rtcb_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE157960_2_v_3_progesterone_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
GSE202434,GSE202438_10_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
HCC202	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.07481
Pancreatic adenocarcinoma_PAAD_TCGA-IB-7893-01A-11R-2204-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2695_KO_SET1B_SRP089784	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.71673
POLR2A_HeLa-S3_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
STAT3-24763339-IMN-ESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
GTEX-QLQW-0126-SM-447BK	GTEx Tissue Sample Gene Expression Profiles	1.0	0.843461
Perturb_5654_KD_FLI1_SRP117628	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.9837
FOXA2	ENCODE Transcription Factor Targets	1.0	null
Perturb_7111_KO_Atf4_SRP344236	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-6.29903
PRSS50	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.28729
Perturb_2772_KD_PRRX1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
CTCF_fibroblast of pedal digit skin_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Respiratory system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.976
KLF4	ChEA Transcription Factor Targets	1.0	null
appears	GeneRIF Biological Term Annotations	1.0	null
IGROV-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.12144
PCIF1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.44132
Medulloblastoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.531
anterior pretectal nucleus, ventral core part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.1223
GSE228181_4_v_1_idh1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC6683136-41598_2019_47363_MOESM4_ESM.xlsx-GENE_SET-Positive_correlation_of_ZEB1_and_other_genes_ZEB1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_8261_KD_RPS2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.7055
GSE209898,GSE209899_0_v_1_trametinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MYC-30127528-KELLY-HUMAN-BRAIN-NEUROBLASTOMA	ChEA Transcription Factor Targets 2022	1.0	null
DAUDI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.84877
GSE108500_1_v_0_foxp1_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE114690_1_v_0_tnfsf14_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
NFIC	ENCODE Transcription Factor Targets	1.0	null
Perturb_13834_KD_RYK_SRP131789	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.70492
GSE146074_9_v_3_ly6e_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
RXRA	ENCODE Transcription Factor Targets	1.0	null
VZ in superolateral temporal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.29169
H3K4me1_G1E_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
GSE247862,GSE247863_0_v_1_eomes_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC11046918-12967_2024_5211_MOESM5_ESM.xlsx-B_FUS-DDIT3-eGFP_vs_WT-Table_S3_Regulated_genes_between_scaffold-cultured_HT1080_FUS_DDIT3-eGFP_cells_and_control_cell_lines_DDIT3	Rummagene Transcription Factor Associations 2026	1.0	null
COLO 680N	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.1129
GSE161295_0_v_1_cdk8_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
CHAGO-K-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.832953
MAX_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15456_KO_GPRC5A_SRP165862	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.4903
18427120-DataS4	GeneSigDB Published Gene Signatures	1.0	null
NCI-H1437	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.867892
Lingula (I), granular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.20746
18794137-SuppTable1a	GeneSigDB Published Gene Signatures	1.0	null
GSE211215_1_v_0_akr1b1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Orbital area, medial part, layer 2	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.56012
HCC2885	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
Bladder Urothelial Carcinoma_BLCA_TCGA-DK-A3X1-01A-12R-A22U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
SK-MEL-28	COSMIC Cell Line Gene Mutation Profiles	1.0	null
LN-229	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.865561
GSE159937_1_v_0_tfcp2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_retinal pigment epithelial cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_GM12867_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE126345_11_v_5_hcrt_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GTEX-QVUS-0011-R10A-SM-3GIK3	GTEx Tissue Sample Gene Expression Profiles	1.0	1.10292
MYCN-18555785-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
ZNF263	ENCODE Transcription Factor Targets	1.0	null
Perturb_16494_KD_RBM39_SRP301121	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_1197_KO_Klf13_SRP302435	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-2.21225
Muscle - Skeletal	GTEx Tissue Gene Expression Profiles 2023	1.0	1.72335
GSE155567_3_v_0_cd33_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_7935_KO_VTRNA1_SRP252980	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	16.9129
Pheochromocytoma and Paraganglioma_PCPG_TCGA-QR-A70E-01A-11R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
female reproductive system	TISSUES Experimental Tissue Protein Expression Evidence Scores	1.0	0.766457
Rdw - Red Blood Cell Distribution Width Result	DisGeNET Gene-Phenotype Associations	1.0	null
CTCF_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8098_KD_TUFM_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.4269
OUMS-23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.943636
GSE86507,GSE86509_0_v_8_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K9ac_HepG2_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_GM12892_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2A_HGPS cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_G1E-ER4_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
UBC13-UEV1A complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.984
LSM10	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.21987
Perturb_15186_KD_CPSF1_SRP186931	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_2586_KD_RORC_SRP066204	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.624
H3K4me3_small intestine_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
SMC3_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
20035825-TableS4b	GeneSigDB Published Gene Signatures	1.0	null
CUX1	ENCODE Transcription Factor Targets	1.0	null
CTCF_GM12870_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
mediodorsal nucleus of thalamus_10 mos_M_12977	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.97771
RT4	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.934792
A172	DepMap CRISPR Gene Dependency	1.0	3.49225
POLR2AphosphoS5_SK-N-MC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE151090_0_v_3_verteporfin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC8052288-mmc4.xlsx-PAF-DREAM-Lung_Poor_Survival-Unnamed_2_KCNIP3	Rummagene Transcription Factor Associations 2026	1.0	null
FOXD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.95
16484322-SuppTable3	GeneSigDB Published Gene Signatures	1.0	null
GSE125014_1_v_4_enzalutamide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Retrosplenial area, lateral agranular part, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.14756
RIF1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.63134
eGFP-GATA2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_fibroblast of skin of abdomen_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
G130	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32505
Perturb_2599_OE_PTH1R_SRP132981	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.94315
H3K4me3_WI38_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-RNOR-0011-R9A-SM-2TF52	GTEx Tissue Sample Gene Expression Profiles	1.0	1.41429
H3K9ac_K562_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8267_KD_FAM120A_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.51555
FOXG1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5736
CP in rostral hippocampus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.43897
GSE179880_2_v_5_e2f4_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NOL8	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.35797
Autonomic nervous system neoplasm	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.314
ventral posterolateral nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.01762
H3K4me3_K562_hg19_4	ENCODE Histone Modification Site Profiles	1.0	null
H2AFZ_astrocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE245134_0_v_1_atg5_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
basal nucleus of Meynert	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.843621
Perturb_15477_OE_MYC_SRP218384	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.52482
GSE48812_9_v_5_sulforaphane_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE191015_0_v_2_gsdmb_human	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC8481886-Table_2.xlsx-A_subsets-AF_MSC_UdRPC_HSC_MSC	Rummagene Transcription Factor Associations 2026	1.0	null
SIN3A_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2AphosphoS5_GM12891_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
VIIB, left, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.9564
MBD3-35695185-NICBASALROOTGANGLIA-MOUSE-EMBRYO	ChEA Transcription Factor Targets 2022	1.0	null
GSE206516,GSE206518_5_v_7_ptdss2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
BFTC-905	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.19729
Perturb_6442_KO_RHO_SRP134183	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.77143
Intestinal cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.74
Head and Neck squamous cell carcinoma_HNSC_TCGA-BB-7871-01A-11R-2232-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
SNTB2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.48393
Bronchogenic carcinoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.585
superficial stratum of AOD	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07354
TBK1_druginhibition_188_GSE53658	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	1.0	1.39786
RDES	CCLE Cell Line Gene CNV Profiles	-1.0	-1.50978
GTEX-T5JC-0011-R8A-SM-32PLM	GTEx Tissue Sample Gene Expression Profiles	1.0	1.00862
Retinoblastoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.697
ASH-3	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Perturb_7232_KO_ADIPOR2_SRP285935	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.46169
GSE113106_0_v_4_dnm2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_12364_KD_SON_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.32502
GTEX-WWYW-0011-R1A-SM-3TW8G	GTEx Tissue Sample Gene Expression Profiles	1.0	1.15038
p53	GeneRIF Biological Term Annotations	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A51F-06A-11R-A266-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2523_KO_TET2_SRP163132	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.37167
GSE102505_6_v_2_tunicamycin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PPME1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.3589
MFE296	DepMap CRISPR Gene Dependency	1.0	5.18013
Eye cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.685
GSE111385_0_v_1_tgfbr2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Posaconazole_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.020275
H3K27ac_limb_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
accessory entopeduncular nucleus (post-migratory)	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.11886
GSE226397_0_v_1_cystine_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
PRKAA2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.50821
KYSE-270	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72905
SUZ12	ENCODE Transcription Factor Targets	1.0	null
GSE216043_10_v_8_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE81803,GSE81912_3_v_1_fmr1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
MYC_Activation - 24 hours_GDS2025_726_mouse_Pancreatic islet beta cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
11823860-SuppTable3	GeneSigDB Published Gene Signatures	1.0	null
GSE126345_7_v_5_hcrt_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC5263239-mmc2.xls-SEM_siMLL-AF4-MLL-AF4_gene_targets_with_decrease_in_MLL-AF4_ChIP-seq_signal_2198_unique_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
CTNNB1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.23629
GSE88819_11_v_4_tug1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
FABP3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.25416
Perturb_8204_KD_IGF2BP1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.96423
H3K4me3_B cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_17629_KO_TAOK1_SRP153109	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.99025
GSE126463_5_v_2_pomalidomide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_14625_KO_OGT_SRP146064	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.87558
Perturb_2425_KD_BNC2_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.16108
Perturb_8212_KD_SMNDC1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.07239
regulation of I-kappaB kinase/NF-kappaB signaling	GO Biological Process Annotations 2023	1.0	null
H3K27ac_fibroblast of lung_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE229973_3_v_5_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me3_Duodenum Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
skeletalmuscle_e	HPA Tissue Sample Gene Expression Profiles	-1.0	-2.07549
ATOH7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.3248
LXFL529	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.936582
Lower respiratory tract disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.908
Perturb_8737_KD_DDX3X_SRP198641	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.71699
MEF2D	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.2169
superior colliculus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.864925
GSE171175,GSE171181_1_v_0_e7107_human	RummaGEO Drug Perturbation Signatures	1.0	null
CP in temporal polar cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.35035
Perturb_13942_KD_CDK12_SRP168173	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.43711
GSE244072_4_v_6_tfeb_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Cortical amygdalar area, posterior part, lateral zone, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.28446
promoting	GeneRIF Biological Term Annotations	1.0	null
H3K4me3_WI38_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
CCNT2	ENCODE Transcription Factor Targets	1.0	null
GSE124097_3_v_0_trem2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
REST_SK-N-SH_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_foreskin fibroblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXP1-21924763-HESC-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
outer SZ in caudal midinferior temporal cortex (area TF)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.902993
Perturb_9479_KO_Mecp2_SRP154883	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	7.49219
GSE159893_2_v_1_genistein_human	RummaGEO Drug Perturbation Signatures	-1.0	null
E2F6	ENCODE Transcription Factor Targets	1.0	null
GSE154767_4_v_0_adam10_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
FOXP1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.1732
POU3F3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.8367
Perturb_8155_KD_DDX59_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.6782
membrane part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
H3K27ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
A2058	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.24494
Perturb_8334_KD_HCF1_SRP178073	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.87665
MEF2A	ENCODE Transcription Factor Targets	1.0	null
H3K4me3_GM12866_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
posterior (caudal) superior temporal cortex (area 22c)_37 pcw_M_263195015	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.830203
Perturb_7663_KD_hnRNPC_SRP076733	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.14498
PMC5554756__F2	PFOCR Pathway Figure Associations 2024	1.0	null
Perturb_6774_Mut_MEF2D_SRP343264	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.73891
HCC1599	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.59259
Perturb_2697_KO_ADIPOR1_SRP089784	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.02888
Validated nuclear estrogen receptor alpha network	PID Pathways	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-H4-A2HQ-01A-11R-A180-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GTF2F1_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
layer 4 of RSC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.22454
GSE144115_2_v_3_stag2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
HDAC2_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
negative regulation of signal transduction	GO Biological Process Annotations 2015	1.0	null
HOXD9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.2314
Perturb_8736_KD_SREBF1_SRP169608	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.59965
Prostate adenocarcinoma_PRAD_TCGA-FC-A4JI-01A-11R-A250-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_10232_KO_RN7SK_SRP201495	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.201
Perturb_6291_KO_ZNF165_SRP390251	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.61928
hsa-miR-15a	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.965816
GSE169697,GSE169725_1_v_4_prrx1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Ubp3-Bre5 deubiquitination complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.785
Perturb_7566_OE_NUDT21_SRP327319	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.98325
HCC2218	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.65732
Perturb_15348_KD_SMARCD3_SRP329316	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.53846
H3K4me3_kidney_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
USF1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me1_Adult Kidney	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
POLR2A_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15399_KD_RUVBL1_SRP361862	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	14.5547
Pancreatic adenocarcinoma_PAAD_TCGA-IB-AAUP-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE201217_3_v_6_usf2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
posteroventral (inferior) parietal cortex_18 yrs_M_12984	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.52211
Piriform-amygdalar area, molecular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.50804
GSE173232_1_v_0_sf3b1_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE162276_5_v_3_pparg_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
terete nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.23075
Male reproductive system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.7
Perturb_12724_KO_BRG1/BRM_SRP255094	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.47752
PROP1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.0558
spleen	GTEx Tissue Gene Expression Profiles	1.0	0.989175
GSE188870,GSE188871_1_v_3_kat7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me1_ES-E14_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
WHSC1	ENCODE Transcription Factor Targets	1.0	null
HOXB7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.163
USF2_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Alzheimer Disease	DisGeNET Gene-Disease Associations	1.0	null
GSE229914_1_v_3_keap1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
VMRCRCZ	CCLE Cell Line Gene Expression Profiles	1.0	1.3514
GSE48812_2_v_5_sulforaphane_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Superior central nucleus raphe	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.95749
anterior cortical nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.999413
H3K4me3_CD19 Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
496100346_FWM_no dementia_TBI_81_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.65443
CTCF_BJ_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ventrolateral prefrontal cortex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.3522
SRF	ENCODE Transcription Factor Targets	1.0	null
Perturb_1049_OE_SMARCD1_SRP269167	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_16811_OE_HNF1A/FOXA3/PROX1_SRP167105	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.9724
SZ in caudal cingulate cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.841238
H2BK120ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
ZNF317	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	40.5211
GSE235587_2_v_1_mitoxantrone_human	RummaGEO Drug Perturbation Signatures	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-HT-7902-01A-12R-2403-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE241036_4_v_1_ethanol_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_7933_KD_Spt6_SRP132004	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.9974
OVISE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.29323
RCOR1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.869532
C4II	DepMap CRISPR Gene Dependency	1.0	2.00851
Poisoning	CTD Gene-Disease Associations	1.0	1.53234
Perturb_3627_KO_HDAC2_SRP355605	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GTEX-QMR6-0011-R7A-SM-32PKL	GTEx Tissue Sample Gene Expression Profiles	1.0	1.67883
GTEX-T6MN-0011-R8A-SM-32QP3	GTEx Tissue Sample Gene Expression Profiles	1.0	1.32934
H3K9me3_endothelial cell of umbilical vein_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_A549_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
MFE280	DepMap CRISPR Gene Dependency	1.0	3.0555
PML_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_GM06990_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_6408_KD_LINC00152_SRP134387	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.52003
GSE142684_0_v_1_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_12910_KD_FOXA1_SRP313175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.6813
H2AFZ_fibroblast of dermis_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SW1990	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-2.88513
CTCF_GM19240_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
JUND	ENCODE Transcription Factor Targets	1.0	null
SETDB1_U2OS_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
negative regulation of i-kappab kinase/nf-kappab signaling	GO Biological Process Annotations 2015	1.0	null
STAT3_MCF 10A_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-QDT8-0011-R8A-SM-32PKE	GTEx Tissue Sample Gene Expression Profiles	1.0	1.60904
Perturb_1319_KO_IRF4_SRP201368	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.45193
OAW28	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.57495
Perturb_3793_KD_SNTA1_SRP057613	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.84094
Perturb_11687_KD_RRM2_SRP212736	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-18.0044
Perturb_8786_Mut_HNF6_SRP217514	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.06804
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00091
intermediate stratum of r2BM	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.27814
CTCF_fibroblast of lung_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6765_KD_PAF1_SRP103746	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.89166
BACH1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_epithelial cell of proximal tubule_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_6063_KD_RIF1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE240344_1_v_0_uxs1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
LHX5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.7793
nucleus subceruleus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.997175
GSE213632_3_v_5_acod1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE155567_1_v_0_cd33_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Stomach Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
CTCF-31629814-HEPATOCYTES-MOUSE-TYROSINEMIA	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_8160_KD_NSUN2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.83496
COLO-783	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.961162
CCP110	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.19519
LHX8_Deficiency_GDS3254_600_mouse_Newborn ovaries	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
OLIG2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.1469
SLC39A8	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.89873
H3K4me3_cardiac mesoderm_hg19_4	ENCODE Histone Modification Site Profiles	1.0	null
CREM-20920259-GC1-SPG-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
SOX9-24532713-HFSC-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
CTCF_kidney epithelial cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SAP30	ENCODE Transcription Factor Targets	1.0	null
Sensory system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.037
Cell type cancer	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
PAX6	ChEA Transcription Factor Targets	1.0	null
GSE160083,GSE160084_2_v_0_tamoxifen_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
hsa-miR-4766-3p	TargetScan Predicted Conserved microRNA Targets	1.0	0.90397
septopallidal core nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.81661
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79163
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
H3K27ac_bone marrow macrophage_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
ZBTB12	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.1112
CTCF_myotube_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2A_GM12892_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H2347	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.65637
Perturb_13867_KD_KDM6B_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_2565_OE_JUN_SRP188712	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.0292
NFIC_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
sirolimus_mus musculus_gpl1261_gse5332	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
Perturb_7665_KO_SNORD45C_SRP257547	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.79523
adrenal gland	GTEx Tissue Gene Expression Profiles	-1.0	-1.20581
H3K4me2_H1 BMP4 Derived Trophoblast Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
SJSA1	CCLE Cell Line Gene Expression Profiles	1.0	1.94282
Disease	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.687
TAF1_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE135352_2_v_3_napabucasin_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE211177,GSE211178_9_v_11_ets1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
TCF12_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE231648_1_v_5_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K9ac_mammary epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_13370_KD_NR1D1_ERP118284	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.79797
hsa-miR-4483	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.809003
upper (rostral) rhombic lip	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.85643
Bed nuclei of the stria terminalis	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.23958
Perturb_825_KD_REST_SRP093671	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.19899
Perturb_32_OE_ERG/MYC_SRP069177	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.24843
PMC6433273-pone.0214296.s009.xlsx-Table_D-S4_Table_Differentially_expressed_mRNAs_in_human_primary_monocytes_after_24_hours_of_LPS_stimulation_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_13692_KD_NSD2_SRP064418	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.0716
Perturb_15021_KD_RelA_SRP078053	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
MAZ_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.307
GLRX3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.50603
H3K4me3_fibroblast of gingiva_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Secondary motor area, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-3.02678
Perturb_11533_KD_ATAC1_SRP109127	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
6351_PIK3C2A_ENST00000265970.7	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.570113
CTCF_GM19239_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TIGD3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.42284
PMC4872073-supp_gkv1528_nar-02930-x-2015-File004.xlsx-Table_S2C-CREB1_FoxA1_Target_Genes_CREB1	Rummagene Transcription Factor Associations 2026	1.0	null
A-427	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.58957
TEAD4-22529382-TROPHECTODERM-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
GSE242199_6_v_5_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
OAW-28	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
H3K9me3_fibroblast of lung_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_12270_KD_EIF4G2_SRP149421	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.08452
lateral ganglionic eminence_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	2.19931
SNU-1040	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Lung adenocarcinoma_LUAD_TCGA-78-7155-01A-11R-2039-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_8078_KD_DAZAP1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
RUSC2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.13595
H3K4me3_Panc1_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
MYC_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8336_KD_CTNNB1_SRP213717	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.7077
H3K4me3_HCT116_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Acute Myeloid Leukemia_LAML_TCGA-AB-2955-03A-01T-0734-13	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE183413_1_v_2_ash1l_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE159937_2_v_0_tfcp2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_GM12865_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_U-87 MG_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE252857_1_v_3_prednisone_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
GSE140937,GSE140938_0_v_2_slfn11_human	RummaGEO Gene Perturbation Signatures	-1.0	null
TCF12_ECC-1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-3133	TargetScan Predicted Conserved microRNA Targets	1.0	1.26663
Umbilical cord cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.545
plicamycin_homo sapiens_gpl570_gse25127	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
Perturb_15439_KD_NUSAP1_SRP074246	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_17691_KD_MDMX_SRP393452	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-15.0581
Perturb_2628_OE_HPGD_SRP292282	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.2338
Zinc finger, RING-type, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
GSE65617_5_v_3_aire_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GTEX-WL46-0011-R9A-SM-3MJFP	GTEx Tissue Sample Gene Expression Profiles	1.0	3.10945
Autosomal genetic disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.053
H3K4me1_testis_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_16727_KO_Mbd2_SRP326773	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-6.25327
Liver hepatocellular carcinoma_LIHC_TCGA-DD-A4NH-01A-11R-A27V-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Artery disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.05
Perturb_6618_KO_NEUROD1_SRP388830	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.4243
DLD-1 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.054
Perturb_8706_KD_SIRT1_SRP267968	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.20987
GSE226249_0_v_7_pirfenidone_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_11429_OE_WWTR1/FOSL1_SRP360169	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.65892
subpretectal nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.24603
SRF_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-4677-5p	TargetScan Predicted Conserved microRNA Targets	1.0	0.49473
Perturb_14903_KO_PRMT6_SRP125977	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.09213
H3K4me3_BJ_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-GC-A3RB-01A-12R-A220-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC10251551-12885_2023_11010_MOESM4_ESM.pdf-38-ZNF605_ZNF605	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_756_KO_DNMT1_SRP389363	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.79154
GSE111385_2_v_3_tgfbr2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE236497,GSE236500_1_v_0_pemrametostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-VS-A8QA-01A-11R-A37O-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_7328_KO_KMT2C_SRP108473	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.79525
GSE225982_2_v_0_ezetimibe_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_2459_KD_GATA3_SRP268806	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
NCIH211	CCLE Cell Line Gene CNV Profiles	-1.0	-1.83629
Perturb_14103_KD_HNRNPC_SRP274546	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.52009
CTCF_fibroblast of upper leg skin_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MAFK_HepG2_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SP4_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE208254_3_v_1_irf8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_7211_Mut_MED26_SRP164752	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
POLR2AphosphoS2_myocyte_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6684_KD_SMARCA2_SRP378606	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE158458_2_v_1_sorafenib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Pheochromocytoma and Paraganglioma_PCPG_TCGA-RW-A68D-01A-11R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
mantle zone of THyB-I	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.14756
pertains	GeneRIF Biological Term Annotations	1.0	null
CREB1	ENCODE Transcription Factor Targets	1.0	null
Perturb_16973_KD_CDK4/FYN_SRP190631	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K4me1_heart_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
GSE146074_9_v_11_ly6e_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE232624_4_v_5_ethanol_human	RummaGEO Drug Perturbation Signatures	1.0	null
POLR2A_ECC-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
UKE-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.39577
Perturb_2766_KD_CNBP_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
CTCF_endothelial cell of umbilical vein_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
RAX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.2769
H3K4me3_cardiac mesoderm_hg19_5	ENCODE Histone Modification Site Profiles	1.0	null
organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
GTEX-TSE9-0011-R8A-SM-3DB7R	GTEx Tissue Sample Gene Expression Profiles	1.0	1.16554
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
Perturb_11435_KD_CIT_SRP173646	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.9626
ZNF143_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
r6 part of dorsal cochlear nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07214
Perturb_468_KD_ADAR2_SRP253895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K4me3_GM12878_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
DMS 273	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.02951
quetiapine_mus musculus_gpl1261_gse45229	GEO Signatures of Differentially Expressed Genes for Small Molecules	-1.0	null
Perturb_2329_KD_SF3B5_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.19639
FOXM1_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE113734_1_v_0_qprt_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H2AFZ_keratinocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE228430_1_v_3_fabp5_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE142684_3_v_5_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_3573_KD_JAB1_SRP222371	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_6260_KD_NDP_SRP188348	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Baicalin_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0130665
Perturb_12960_KD_YTHDC1_SRP309987	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GTF2B	ENCODE Transcription Factor Targets	1.0	null
MYBL1	ChEA Transcription Factor Targets	1.0	null
Perturb_7373_KD_PATL1_ERP022060	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.37037
POLR2A_K562_hg19_8	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_17641_OE_YAP_SRP298391	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE129241_3_v_6_valproic acid_human	RummaGEO Drug Perturbation Signatures	1.0	null
Colon cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.238
MRK-NU-1	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Perturb_8718_KD_RPL39_SRP385284	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.7302
SFT2D1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.23727
GSE89729_0_v_1_ppard_human	RummaGEO Gene Perturbation Signatures	-1.0	null
cellular_component	LOCATE Predicted Protein Localization Annotations	1.0	null
tonsil_8a1	HPA Tissue Sample Gene Expression Profiles	1.0	1.50871
Perturb_665_KO_Myc_SRP093784	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	3.86315
GSE158632_3_v_0_oxyquinoline_human	RummaGEO Drug Perturbation Signatures	-1.0	null
superficial stratum of OB	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.51172
Lung adenocarcinoma_LUAD_TCGA-55-A4DF-01A-11R-A24H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Secondary Malignant Neoplasm Of Lymph Node	DisGeNET Gene-Disease Associations	1.0	null
GSE242199_9_v_3_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE48812_11_v_10_sulforaphane_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K9ac_keratinocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Lung adenocarcinoma_LUAD_TCGA-50-6590-01A-12R-1858-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-10_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
PMC12224929-ADVS-12-2416784-s006.xlsx-DEG_circGLIS3_KD-Unnamed_6_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Proventriculus	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.575
EZH2_mammary epithelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-HT-8558-01A-21R-2404-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-HW-7486-01A-11R-2027-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE169356_0_v_3_ivermectin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
TMEM177	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.72514
GTEX-X4XX-0011-R3B-SM-46MWK	GTEx Tissue Sample Gene Expression Profiles	1.0	1.02698
GEMIN4	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.55351
H3K4me3_B cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
7538_RPS8_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.511174
GTEX-OXRO-1726-SM-3LK6C	GTEx Tissue Sample Gene Expression Profiles	1.0	1.18897
RPL27	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.08451
CALU-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.867892
Perturb_8274_KD_SERBP1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.4703
9426_TUBGCP3_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.785499
OVSAHO	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.943636
Perturb_6259_KD_NDP_SRP188348	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
NUDT13	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.30101
H3K4me3_heart_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_2765_KD_BNC2_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.46575
Perturb_3884_KD_CTR_SRP124930	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.88921
Perturb_8162_KD_SNRNP70_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.77155
H3K4me2_A549_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me1_K562_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_3866_KD_MEF2D_SRP333146	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.85368
H3K4me1_keratinocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Red Cell Distribution Width Determination	DisGeNET Gene-Phenotype Associations	1.0	null
GSE93674_2_v_0_ezh2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H2AK5ac_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_2533_KO_HSF1_SRP341615	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Bed nuclei of the stria terminalis, anterior division	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.52988
Superior colliculus, zonal layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.09269
U2OS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.42548
Stomach disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.818
TCF3_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-B0-4699-01A-01R-1277-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GFI1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9881
H3K4me1_G1E-ER4_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
intermediate stratum of SeDg	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.37401
OVK-18	COSMIC Cell Line Gene Mutation Profiles	1.0	null
laterostriatal stripe	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.10494
SOX18	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.07161
septostriatal part of the olfactory tuberculum	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.58806
Anterior cingulate area, dorsal part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.26536
PMC7206068__F3	PFOCR Pathway Figure Associations 2023	1.0	null
Perturb_398_KD_WTAP_SRP039397	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.06979
GSE200352_1_v_8_pparg_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
SP4	ENCODE Transcription Factor Targets	1.0	null
Main olfactory bulb, glomerular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.72548
BT549	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	-1.0	-1.63104
Perturb_2067_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.80684
Perturb_4177_KO_Dnmt1_SRP043000	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-12.0585
GSE147893,GSE147897_2_v_1_rbm4_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_HeLa-S3_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.27195
EP300_H1-hESC_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_5652_Mut_SA1_SRP133292	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.85433
GSE117730,GSE117732_0_v_2_apobec2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
HSD17B4_KO_GDS3468_503_mouse_liver	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
GSE254517_1_v_0_irf7_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_14630_KD_MSI1_SRP067129	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.29645
PMC3607232-mmc1.xls-RS411_SEM_common_AF4_MLLN_K79Me-MLL_AF4_H3K79me3_SEM_n_2490_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
NCI-H1623	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.986907
Graves' disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.133
CAPAN-1	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
CTCF_CH12.LX_mm9_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Sarcoma_SARC_TCGA-HS-A5N9-01A-11R-A26T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE193900,GSE193905_1_v_0_pura_human	RummaGEO Gene Perturbation Signatures	1.0	null
MXI1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
BICR22	CCLE Cell Line Gene CNV Profiles	1.0	3.27615
Perturb_5648_KO_PHF19_SRP142503	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.0315
Head and Neck squamous cell carcinoma_HNSC_TCGA-CV-7430-01A-11R-2132-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HOXD10	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.8956
TAF7_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE205976,GSE205978_1_v_4_cep83_human	RummaGEO Gene Perturbation Signatures	1.0	null
H3K27ac_heart_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TCF12_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Enterovirus 71_4Hour_None_GSE15323	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-0.813945
LDB1-21186366-BM-HSCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
ChIP_KLF4_18555785	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
pRb_Deficiency_GDS3176_605_mouse_Skin	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GTEX-UTHO-0011-R1A-SM-3GIJO	GTEx Tissue Sample Gene Expression Profiles	1.0	1.40296
ATOH7	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.00861
H3K4me3_CD3 Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE122215,GSE122217_0_v_4_peg10_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_9648_KD_TCF7L2_SRP327946	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.03809
H3K4me3_fibroblast of pedal digit skin_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE231891_1_v_4_cdk8_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE231648_4_v_3_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE111247_11_v_10_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE176093_0_v_1_mineral oil_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
CLN6	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	4.24607
Perturb_13896_KO_TLR3/MYD88_SRP332441	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.56424
SARS-CoV MA15_Day4-PFU-10^3_None_GSE33266	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-2.47038
Frontal pole, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.72846
SIX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.9789
H3K4me1_K562_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
HDAC1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_10212_KD_SETX_SRP353945	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.40028
RKO-E6	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.953477
SOX18	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.328
GSE128844_0_v_1_chloroquine_human	RummaGEO Drug Perturbation Signatures	1.0	null
Thoracic cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.792
BICR 31	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.48038
island of Calleja major	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.78263
Feather calamus	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.847
GTEX-QDT8-2926-SM-32PKC	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09027
Perturb_9151_KD_DDX21_SRP327839	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.93836
Perturb_15560_KO_SLFN11_SRP327912	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_6871_KD_HHEX_SRP323378	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.7033
PMC3290552-pone.0032232.s006.xls-MUC4-KD_vs_Mock-Unnamed_3_AR	Rummagene Transcription Factor Associations 2026	1.0	null
IQSEC2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.57799
GSE58724_1_v_4_oxymetholone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
RAD21_A549_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GATA1_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TCF12_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
VZ in subgenual cingulate neocortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.01554
Perturb_13866_KD_KDM6B_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_8705_KD_SIRT1_SRP267968	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.85699
GSE224311_3_v_1_chaetocin_human	RummaGEO Drug Perturbation Signatures	1.0	null
POLR2A_endothelial cell of umbilical vein_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_1298_KO_SOX15_SRP049465	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.37276
GSE139455_2_v_5_stat3_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE198165,GSE198166_5_v_3_zfp266_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Bile duct cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.433
FOXM1_MCF-7_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HOXC9-25013753-NEUROBLASTOMA BE2-C-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
SMC3	ENCODE Transcription Factor Targets	1.0	null
Perturb_2309_KD_DHX8_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.53096
SNU626	CCLE Cell Line Gene CNV Profiles	-1.0	-1.50879
Brain Lower Grade Glioma_LGG_TCGA-DU-5872-02A-21R-A36H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
ZNF35	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.8182
Perturb_8752_KD_ANLN_SRP083014	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.5554
GSE202933_1_v_0_ugt2b28_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE246911,GSE246913_4_v_1_arid1a_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
RAD21_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8339_OE_MSI1_SRP219036	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
CTCF_cardiac fibroblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ARL6IP5	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.018
POLR2A_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H2110	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	1.0	null
H3K4me3_MEL cell line_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
Liver Diseases	CTD Gene-Disease Associations	1.0	1.32726
Perturb_8702_KD_MXD4_SRP374659	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	18.0
GSE102269_1_v_2_clpp_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
2966_FANCI_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.555397
Orbital area, medial part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.78388
GSE92457_9_v_10_ethanol_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
SETDB1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF384_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SK-MEL-31	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.7382
Prostate adenocarcinoma_PRAD_TCGA-KK-A8IK-01A-11R-A36G-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_13044_OE_FUS_SRP069787	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.34096
Perturb_6836_KO_METTL3_SRP193002	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.71873
medial ganglionic eminence_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	2.08226
Lymphoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.265
SIN3A_Panc1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.939202
dorsolateral prefrontal cortex_37 pcw_M_263195015	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.01693
GTEX-Q2AG-0011-R9A-SM-2HMJ6	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09404
Kidney renal papillary cell carcinoma_KIRP_TCGA-HE-7130-01A-11R-1965-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Bimatoprost_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0212352
GSE149355_0_v_1_esrp1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE157960_0_v_1_progesterone_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
POLR2AphosphoS5_neural cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney Chromophobe_KICH_TCGA-KL-8341-01A-11R-2315-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
SOX9-24532713-HFSC-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
hsa-miR-1179	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
Bed nuclei of the stria terminalis, anterior division, oval nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.46597
Plant cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.938
GSE165689_0_v_1_zcchc8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE233183,GSE233187_3_v_6_larp1_human	RummaGEO Gene Perturbation Signatures	1.0	null
HEC251	DepMap CRISPR Gene Dependency	1.0	3.11669
A-CA-04-2009(H1N1)_12Hour_23935999_GSE47960	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.353
59M	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.18533
NCBP2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.21761
GSE102757_1_v_0_panobinostat_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Posterior limiting nucleus of the thalamus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.29619
GSE142430_3_v_0_prmt5_human	RummaGEO Gene Perturbation Signatures	-1.0	null
SP1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27ac_H1-hESC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
PMC6786946-NIHMS1535503-supplement-3.xlsx-SAT1_2_0x-FOXM1_genes_FOXM1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_2776_KD_YBX1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
POLR2A_H1-hESC_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
COLO680N	DepMap CRISPR Gene Dependency	1.0	5.08141
GTEX-U4B1-0006-SM-3DB8E	GTEx Tissue Sample Gene Expression Profiles	1.0	0.873551
H2AFZ_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Retrosplenial area, dorsal part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.11725
MDAMB436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.69631
Perturb_2562_OE_JUN_SRP188712	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
superficial stratum of THyB-P	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.2316
cell part	GO Cellular Component Annotations 2015	1.0	null
hsa-miR-769-5p	MiRTarBase microRNA Targets	1.0	null
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Combined-MYB_Combined_sgRNA_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
TAL1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-4778-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
DLX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.9389
TEAD4_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-XLM4-0011-R2B-SM-4AT5Z	GTEx Tissue Sample Gene Expression Profiles	1.0	1.34836
CTCF_GM06990_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-EJ-7792-01A-11R-2118-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE195568_1_v_10_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
THP1	CCLE Cell Line Gene Expression Profiles	1.0	1.40148
Perturb_8217_KD_U2AF2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.58798
ENL-26711339-SEM-HUMAN-BLOOD-LEUKEMIA	ChEA Transcription Factor Targets 2022	1.0	null
UNCX	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.2945
TFAP2C	JASPAR Predicted Transcription Factor Targets	1.0	null
Lung adenocarcinoma_LUAD_TCGA-55-7913-01B-11R-2241-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_3912_KD_Y14_SRP118481	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Mesothelioma_MESO_TCGA-SC-A6LN-01A-11R-A34F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_467_KD_ADAR1/ADAR2_SRP253895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
UCSD-242L	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.867044
SLAC complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.933
GSE206516,GSE206518_2_v_4_ptdss2_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE119978,GSE180930_2_v_4_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-BT-A20N-01A-11R-A14Y-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me3_SK-N-MC_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
PMC5263239-mmc2.xls-THP-1_-_MLL-AF9-Non-spreading_targets_gene_names_1900_unique_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-EB-A85J-01A-12R-A352-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Head and neck carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.008
Perturb_15441_KD_TMPOAS1_SRP273203	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_9941_KD_MBNL1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.22117
r2 part of median raphe nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	4.00369
Lung squamous cell carcinoma_LUSC_TCGA-77-8009-01A-11R-2187-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
BT-549	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.11685
POLR2A_A549_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6075_KD_SUV39H2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me3_astrocyte of the spinal cord_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
OBF-1_NULL MUTATION_GDS3473_571_mouse_Bone marrow pre-BII cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
Biliary tract cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.462
GSE248045,GSE248046_0_v_5_runx1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NCI-H345	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19386
H2AFZ_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Liver hepatocellular carcinoma_LIHC_TCGA-ED-A5KG-01A-11R-A27V-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_6072_KD_SUMO2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_710_KO_DNMT1_SRP389363	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.774
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.88953
inner portion of medial ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	2.12077
Perturb_8490_KD_CAG/CUG_SRP119324	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Retinal cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.095
FOS	ENCODE Transcription Factor Targets	1.0	null
Tomivosertib_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0172839
MM.1S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.26637
YY1_ECC-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
LIM1215	COSMIC Cell Line Gene Mutation Profiles	1.0	null
hsa-miR-3150a-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
H3K27ac_B cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE232631_5_v_1_brca2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_13016_KO_ALOX5_SRP367905	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
NCIN87	DepMap CRISPR Gene Dependency	1.0	4.33609
CHD4-35695185-NICBASALROOTGANGLIA-MOUSE-EMBRYO	ChEA Transcription Factor Targets 2022	1.0	null
Interferon regulatory factor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.291
GSE126345_2_v_5_hcrt_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC7450072-41598_2020_71096_MOESM1_ESM.xlsx-Table3_SS_vs_AA_MP-Gene_TEAD1	Rummagene Transcription Factor Associations 2026	1.0	null
caudal ganglionic eminence_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.87783
CTCF_keratinocyte_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE206516,GSE206518_3_v_7_ptdss2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
absent extraembryonic coelom	MGI Mouse Phenotype Associations 2023	1.0	null
H3K4me3_skeletal muscle cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
REST_myocyte_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SIRT6_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PBX3_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_5408_OE_LINC00339_SRP302179	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.83634
PMC4904359-12915_2016_267_MOESM12_ESM.xlsx-ARGFX_DOWN-All_significantly_up_regulated_genes_determined_by_DESeq2_fold_change_greater_than_1_25_going_down_from_an_FPKM_of_at_least_2_ARGFX	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_1095_KO_ATXN1L_SRP230198	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.42345
GSE188458_2_v_0_hydrogen peroxide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_3775_KD_DPPA5_SRP041162	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
TRIM28_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ATF2_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6764_KO|KD_SERPINE2_SRP103746	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.34344
Perturb_6840_KD_lncLUCRC_SRP218870	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.46628
ONCODG1	CCLE Cell Line Gene CNV Profiles	1.0	1.53712
CTCF_retinal pigment epithelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-OHPN-0011-R2A-SM-2I5FB	GTEx Tissue Sample Gene Expression Profiles	1.0	1.31675
GTEX-R55E-0011-R9A-SM-2TC6C	GTEx Tissue Sample Gene Expression Profiles	1.0	1.37609
GSE120612_7_v_5_etoposide_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K79me2_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_1302_OE_ERG/MYC_SRP069177	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.70253
Perturb_8087_KD_EIF4G2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.70189
GSE206516,GSE206518_6_v_4_ptdss2_human	RummaGEO Gene Perturbation Signatures	1.0	null
CTCF_K562_hg19_7	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_fibroblast of gingiva_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14391_KD_PAX8_SRP276625	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GTEX-S7SE-0011-R10A-SM-2XCDF	GTEx Tissue Sample Gene Expression Profiles	1.0	0.91048
GSE145476_2_v_0_hopx_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_2556_KO_TET2_SRP163132	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.64179
GATA3-27048872-CHIP-SEQ-THYMUS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
GTEX-N7MS-0011-R2a-SM-2HML6	GTEx Tissue Sample Gene Expression Profiles	1.0	0.994305
GSE149943_2_v_0_cd8a_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC9996951-40659_2023_417_MOESM3_ESM.xlsx-Osteo_vs_MSC_Array2_hypo_er_txt-1_UCSC_NAME_MSC	Rummagene Transcription Factor Associations 2026	1.0	null
EBF1_GM12878_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE169152_3_v_7_ibrutinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
negative regulation of canonical NF-kappaB signal transduction	GO Biological Process Annotations 2025	1.0	null
outer portion of medial ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.66073
GSE133087_1_v_2_metformin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_15044_KD_PTBP1_SRP124244	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_8131_KD_EIF2S1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Disease of anatomical entity	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
SMAD1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-3.12342
TAF7	ENCODE Transcription Factor Targets	1.0	null
Perturb_6078_KD_TARDBP_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.84411
Perturb_511_OE_ACE2_SRP278541	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.155
CTCF_GM12868_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14320_KD_CD95L_SRP111532	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_2071_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.54932
CHD2_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MEF2B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.7788
TE-6	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
Brain Lower Grade Glioma_LGG_TCGA-FG-8187-01A-11R-2256-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
MEOX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.943
Kidney renal papillary cell carcinoma_KIRP_TCGA-BQ-5879-01A-11R-1592-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K9ac_K562_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
TCF7L2_HCT116_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H1792	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.82992
Sarcoma_SARC_TCGA-DX-A3U7-01A-11R-A29R-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE160817_5_v_9_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Male reproductive organ cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.704
Atg1/ULK1 kinase complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.28
pdx1_22135308_duodenum_lof_mouse_gpl1261_gds4348	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.059321
CI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.07015
Liver	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-1.1275
intermediate portion of DFC (area 9/46)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.909263
Liver hepatocellular carcinoma_LIHC_TCGA-BC-A216-01A-11R-A155-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE203329_2_v_1_mettl5_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_9100_KD_Tfpi_SRP312891	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.16072
Perturb_296_OE_ERG/MYC_SRP069177	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.93153
POLR2A_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Right_Atrium	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	-1.0	-1.3624
PMC3355086-pgen.1002728.s003.xlsx-Tabelle1-HEY2_downregulated_HEY2	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_7810_KD_RAM_SRP091113	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.22822
Perturb_2351_KD_CNBP_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
hsa-miR-3908	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
Perturb_8276_KD_UPF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE132948,GSE132949_2_v_3_msi2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PrefrontalCortex	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-1.03995
Perturb_2065_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.6119
Kidney renal clear cell carcinoma_KIRC_TCGA-CZ-5989-01A-11R-1672-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_cardiac muscle cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_fibroblast of lung_hg19_5	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-PLZ5-1726-SM-2I5F6	GTEx Tissue Sample Gene Expression Profiles	1.0	0.877125
Perturb_15401_KD_MELK_SRP098926	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.7055
layer 1 of LOT	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.43819
Perturb_7554_Mut_FUS_SRP302857	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.69165
Perturb_7709_KO_VTRNA1_SRP252980	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.81451
GTEX-RVPV-0011-R11A-SM-2TF6F	GTEx Tissue Sample Gene Expression Profiles	1.0	1.12447
GSE58724_1_v_0_oxymetholone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_9081_KD_XBP1_SRP117686	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.79952
4498_LAMA5_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.5226
Selinexor _NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.013743
Cervical Cancer	DisGeNET Gene-Disease Associations	1.0	null
H3K4me3_Jurkat_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
DMRT1-23473982-TESTES-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_13886_KD_CDK4/CDK6_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE211126_1_v_0_hapln1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE123943_2_v_0_sox1_human	RummaGEO Gene Perturbation Signatures	1.0	null
Sternal cartilage	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.323
SIRT6	ENCODE Transcription Factor Targets	1.0	null
GSE63857_3_v_1_tamoxifen_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me3_keratinocyte_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Oral mucosa	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
CTCF_epithelial cell of proximal tubule_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-WZTO-0011-R11A-SM-4E3K9	GTEx Tissue Sample Gene Expression Profiles	1.0	0.850318
Perturb_8153_KD_BOP1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
r10 part of dorsal parvicellular reticular formation	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.05867
GSE138001_5_v_4_rorb_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CTCF_pancreas_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE125153_1_v_0_bcl3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE174498,GSE174500_3_v_7_asparaginase_human	RummaGEO Drug Perturbation Signatures	-1.0	null
496100577_FWM_probable Alzheimer's disease_TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.00649
Perturb_8096_KD_SRSF5_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
PMC5095001-oncotarget-07-36293-s002.xlsx-Table_S2-Table_S2_MYCN-correlated_genes_and_their_correlations_with_other_transcription_factors_MYCN	Rummagene Transcription Factor Associations 2026	1.0	null
GSE233566_1_v_2_braf_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE235120_1_v_0_pidd1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K9ac_fibroblast of lung_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Liver hepatocellular carcinoma_LIHC_TCGA-CC-A1HT-01A-11R-A131-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
ventral entopeduncular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.23099
CTCF_K562_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
DMS 79	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.46391
Perturb_2773_KD_RPL7_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_9228_OE_HDAC4_SRP334442	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-2.19811
HOXA10	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.2415
GTEX-R55E-0011-R6A-SM-2TC5T	GTEx Tissue Sample Gene Expression Profiles	1.0	1.00991
PAX5_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE176008_0_v_5_azacitidine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE142684_3_v_1_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
THAP1	ENCODE Transcription Factor Targets	1.0	null
GSE247862,GSE247863_4_v_1_eomes_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Pheochromocytoma and Paraganglioma_PCPG_TCGA-PR-A5PG-01A-11R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
SIN3A_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15508_KD_NEDD9_SRP301145	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GTEX-N7MS-0011-R4a-SM-2HMKW	GTEx Tissue Sample Gene Expression Profiles	1.0	2.1856
GSE165916_1_v_2_n4bp1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
POLR2A_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE174498,GSE174500_5_v_7_asparaginase_human	RummaGEO Drug Perturbation Signatures	-1.0	null
E2F1-18555785-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
TCF3_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Cell type cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.96
PMC11046918-12967_2024_5211_MOESM5_ESM.xlsx-A_FUS-DDIT3_vs_both_controls-Table_S3_Regulated_genes_between_scaffold-cultured_HT1080_FUS_DDIT3-eGFP_cells_and_control_cell_lines_DDIT3	Rummagene Transcription Factor Associations 2026	1.0	null
H2AFZ_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
Lung squamous cell carcinoma_LUSC_TCGA-66-2795-01A-02R-0980-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K4me1_heart_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-VM-A8CE-01A-11R-A36H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
NCI-H1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.21214
SETD4	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.057
GSE203158_0_v_13_aire_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Prostate disease	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
PMC8528285-pbio.3001085.s010.xlsx-Fig_7A-MLX_TESTES_MLX	Rummagene Transcription Factor Associations 2026	1.0	null
GSE125153_1_v_3_bcl3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
medial superior olive	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.873461
Perturb_466_KD_ADAR1_SRP253895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE188458_2_v_3_hydrogen peroxide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE235550_2_v_0_hspa9_human	RummaGEO Gene Perturbation Signatures	-1.0	null
59M	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.932553
EZH2_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8209_KD_RPS10_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.04689
putamen	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.0713
Almonertinib (mesylate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0180725
Obstructive sleep apnea_Hepatic Tissue_GSE1873	GEO Signatures of Differentially Expressed Genes for Diseases	1.0	2.10591
temporal neocortex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.23808
MAX_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
A3/KAW	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.832953
GSE246195,GSE246305_1_v_3_sin3a_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Fhm	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.719
Bed nuclei of the stria terminalis, anterior division, anterolateral area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.08224
H3K4me3_Brain Mid Frontal Lobe	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
inner SZ in dorsolateral prefrontal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.966351
CTCF_GM12866_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CCT7	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.66079
H3K27ac_small intestine_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE211177,GSE211178_4_v_3_ets1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
CEBPB_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2A_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
prostate	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	-1.0	-0.89004
GSE218060_7_v_4_decitabine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K4me3_astrocyte of the spinal cord_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
pancreas_6b	HPA Tissue Sample Gene Expression Profiles	-1.0	-1.23409
Skin Cutaneous Melanoma_SKCM_TCGA-ER-A1A1-06A-11R-A18U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Hepatoblastoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.664
GSE254517_3_v_0_irf7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me1_ES-Bruce4_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_spleen_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_brain microvascular endothelial cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hippocampus (hippocampal formation)_12 pcw_F_12960	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.0913
GSE148200_1_v_5_gemcitabine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
layer 5 of RSC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.57836
GSE112860_0_v_2_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_7590_KD_GEMIN5_SRP368027	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	13.8484
NR2F2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-CW-6087-01A-11R-1672-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
RCOR1-19997604-NEURONS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
posterolateral cortical amygdaloid area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.20504
H3K4me3_mammary epithelial cell_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_olfactory bulb_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
MYC_K562_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A1Q4-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE142019,GSE142021_10_v_3_ythdf2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_10107_KD_EIF2S1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.59553
CTCF_foreskin fibroblast_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15214_KD_KLF4_SRP255722	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.44208
H3K4me3_osteoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_2335_KD_SON_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.03268
PMC7818749-12931_2021_1617_MOESM1_ESM.xlsx-TBX4-ENSEMBL_TBX4	Rummagene Transcription Factor Associations 2026	1.0	null
PMC7293310-41467_2020_16179_MOESM8_ESM.xlsx-Table_S9_GATA1_WT24h_vs_SET24-Unnamed_10_GATA1	Rummagene Transcription Factor Associations 2026	1.0	null
reticular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.05101
Perturb_3886_KD_CTR_SRP124930	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.54551
Perturb_6037_KD_MBNL1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE153836_14_v_1_fluoxetine_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
496100277_FWM_no dementia_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.3203
A2780	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.952985
TBL1XR1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
occipital neocortex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.73176
POLR2AphosphoS5_GM12891_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTAGE9	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.4223
Perturb_14893_KO_H11_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.314
GSE142019,GSE142021_1_v_3_ythdf2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_11538_KD_YEATS2_SRP094447	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-19.3979
H3K4me3_keratinocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_brown adipose tissue_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
RCOR1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE185163_5_v_2_clic4_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
SPI1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
6017_P2RY1_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.547283
GSE202434,GSE202438_10_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE195568_2_v_4_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
TCF7L1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.0151
PMC8851354-Table_5.xlsx-FUS-DDIT3_reg_FD-bound-Supplementary_Table_5_Genes_regulated_by_FUS-DDIT3_that_are_FUS-DDIT3_targets_in_MLS_402-91_cells_DDIT3	Rummagene Transcription Factor Associations 2026	1.0	null
C1orf21	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.14675
GSE100102_2_v_6_cgas_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_8450_KD_NPM1_SRP230777	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.8879
Perturb_8192_KD_PARN_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.21867
YY1_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE179036_1_v_0_trim24_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
hsa-miR-215-5p	MiRTarBase microRNA Targets	1.0	null
HCC95	CCLE Cell Line Gene CNV Profiles	1.0	1.86278
H3K4me3_cardiac mesoderm_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Lung adenocarcinoma_LUAD_TCGA-78-7536-01A-11R-2066-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
layer 6b of PaS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.13275
MAZ_IMR-90_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Glioma	DisGeNET Gene-Disease Associations	1.0	null
Disease of mental health	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.005
GSE142210_9_v_0_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE100316_7_v_4_mtor_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_15562_KO_SLFN11_SRP327912	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.18703
Breast disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.79
GSE242199_6_v_11_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC12019518-ao5c02459_si_002.xlsx-Table_S3-Table_S3_Screening_of_genes_that_are_commonly_upregulated_in_cells_on_stiff_substrate_and_down-regulated_by_KD_of_UBE2A_B_AR	Rummagene Transcription Factor Associations 2026	1.0	null
ChIP_KLF4_19030024	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
Perturb_6425_KD_LOC646329_SRP220725	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.46612
ZNF384	ENCODE Transcription Factor Targets	1.0	null
FOXE1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	217.744
Perturb_10667_OE_PAX3FOXO1_SRP371512	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.34931
G59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.22378
GSE161846,GSE161849_1_v_0_smarca4_human	RummaGEO Gene Perturbation Signatures	1.0	null
USF2	ENCODE Transcription Factor Targets	1.0	null
PMC7293310-41467_2020_16179_MOESM8_ESM.xlsx-Table_S9_GATA1_WT24h_vs_SET24-Unnamed_12_GATA1	Rummagene Transcription Factor Associations 2026	1.0	null
Colonic epithelium cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.623
Perturb_17642_OE_YAP_SRP298391	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.97575
VIIIA	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.06248
GATA3_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2436_KD_YBX1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.02509
Lung cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.76
IMR-32	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.855143
Breast Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
Perturb_11524_KD_NRF2_SRP092641	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-19.3979
H3K4me2_endothelial cell of umbilical vein_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
anterior amygdaloid area	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.70155
Network map of SARS CoV 2 signaling	WikiPathways Pathways 2024	1.0	null
Perturb_11406_KD_HNRNPM_SRP143499	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.6543
GSE196259_2_v_3_gcm1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
PAX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	36.0002
RASSF8	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.05552
GSE231648_1_v_3_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me2_CD14-positive monocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE112760,GSE112767_2_v_5_ddx6_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE185944_5_v_4_pth1r_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CTCF_fibroblast of lung_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SIX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.12
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.57411
Childhood Neuroblastoma	DisGeNET Gene-Disease Associations	1.0	null
496100362_FWM_no dementia_no TBI_78_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.40304
Taenia tecta, dorsal part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.3593
OVCAR-4	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.832028
hsa-miR-152	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
GSE195568_6_v_7_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
NCIH2196	CCLE Cell Line Gene CNV Profiles	1.0	2.35032
superficial stratum of PPaA	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.52751
GSE119978,GSE180930_6_v_5_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K4me3_WI38_hg19_4	ENCODE Histone Modification Site Profiles	1.0	null
P300-19829295-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
GSE112763,GSE112767_4_v_3_dgcr8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE119978,GSE180930_2_v_5_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
CTCF_kidney epithelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27ac_endothelial cell of umbilical vein_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
ARID3A	ENCODE Transcription Factor Targets	1.0	null
Interferon regulatory factor 7 complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.713
PML body	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.379
TestisSeminiferousTubule	BioGPS Human Cell Type and Tissue Gene Expression Profiles	1.0	1.45664
FOXP2	ENCODE Transcription Factor Targets	1.0	null
Perturb_12936_KO_SPI1_SRP342114	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.84475
Oligodendrocyte_Brain_Mouse	CellMarker Gene-Cell Type Associations	1.0	null
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.54982
H3K4me3_brain_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE158834_10_v_4_palmitic acid_human	RummaGEO Drug Perturbation Signatures	1.0	null
CUX1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE139966_5_v_3_figla_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Carcinoma Of Lung	DisGeNET Gene-Disease Associations	1.0	null
Taenia tecta, ventral part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.4832
PITX1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.2248
POLR2AphosphoS5_HL-60_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Carcinoma Of Bladder	DisGeNET Gene-Disease Associations	1.0	null
TE6	CCLE Cell Line Gene CNV Profiles	1.0	1.84336
GSE211126_3_v_0_hapln1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_10144_KD_STAU2_SRP216662	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.71224
GSE166783_8_v_2_tp53_human	RummaGEO Gene Perturbation Signatures	-1.0	null
YY1_GM12892_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_foreskin fibroblast_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
intracellular organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
Perturb_16639_KO_Tardbp_SRP278199	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-3.16105
PMC7293310-41467_2020_16179_MOESM8_ESM.xlsx-Table_S9_GATA1_WT24h_vs_SET24-Unnamed_9_GATA1	Rummagene Transcription Factor Associations 2026	1.0	null
daudi	HPA Cell Line Gene Expression Profiles	1.0	1.34963
hsa-miR-148b	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
Perturb_426_KD_FOXM1/MYBL2_SRP239534	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.26621
Brain Lower Grade Glioma_LGG_TCGA-FG-A4MY-01A-11R-A26U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
ATF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8823
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.48376
Brain Lower Grade Glioma_LGG_TCGA-HW-A5KK-01A-11R-A27Q-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_thymus_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_4916_KO_TFAP2A_SRP303667	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.80454
GSE180185_9_v_10_setbp1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
red nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.849877
CTCF_MCF-7_hg19_6	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3177_KO_KDM1A2a_SRP348808	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.54577
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-4_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
hsa-miR-4490	TargetScan Predicted Conserved microRNA Targets	1.0	0.49473
Pancreas disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.398
POLR2AphosphoS5_neural cell_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-X4XX-0011-R8B-SM-46MWM	GTEx Tissue Sample Gene Expression Profiles	1.0	0.881374
GSE226316_0_v_2_tead2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
KLE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.6586
PRKACA_knockout_266_GSE20984	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	-1.0	-1.78389
GSE108326_1_v_0_doxycycline_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE119978,GSE180930_0_v_8_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
15260889-SuppTable2	GeneSigDB Published Gene Signatures	1.0	null
EP300_GM12878_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE152666,GSE152668_2_v_1_carm1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.29726
GTEX-XMD1-0011-R2B-SM-4AT5N	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09511
Female reproductive organ cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.693
GSE210225_0_v_1_inosine_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
upper dorsal lateral hypothalamic area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.42297
multifunctional	GeneRIF Biological Term Annotations	1.0	null
GTEX-Q2AG-0008-SM-48U2K	GTEx Tissue Sample Gene Expression Profiles	1.0	0.988375
GSE124375_13_v_12_chd2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE132948,GSE132949_4_v_1_msi2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
superficial stratum of PSPa	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.23099
GSE149901_2_v_1_anlotinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me3_fibroblast of pedal digit skin_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
PMC4634137-ncomms9549-s7.xlsx-ZF_Hair_cell_data-Unnamed_1_CREBZF	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_2769_KD_FOXQ1_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_6070_KD_SFPQ_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me3_thymus_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_81_KD_CENPA1_SRP187530	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Kidney renal clear cell carcinoma_KIRC_TCGA-BP-4781-01A-01R-1305-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_14883_KO_H11_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.6619
Supraspliceosomal complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.105
superficial stratum of PO1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.44628
Perturb_12946_KD_METTL3_SRP106608	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Nerve Degeneration	CTD Gene-Disease Associations	1.0	1.39366
Perturb_15505_KD_CDK7_SRP179971	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
HCC1576	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00091
Perturb_11403_KD_CPT1A_SRP076884	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.3058
PMC12522211-NIHMS2104691-supplement-MMC1.xlsx-SRCAP_DE_genes-Gene_SRCAP	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_8368_KD_IGF2BP3_SRP094100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.0476
Perturb_6059_KD_RBM26_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GTEX-QVJO-0011-R5A-SM-2S1QM	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09077
GSE226249_0_v_3_pirfenidone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
layer 6 of RSC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.85567
Perturb_13380_KO_CTIP2_SRP150394	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.86423
Perturb_5103_KO_Ssrp1_SRP235595	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	3.88075
BCL3	ENCODE Transcription Factor Targets	1.0	null
GATA1_megakaryocyte_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H1_Derived_Neuronal_Progenitor_Cultured_Cells	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	1.0	0.919137
Perturb_9107_KD_G6PD_SRP287480	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.07372
1395_CDC26_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.525543
reproductive system	TISSUES Experimental Tissue Protein Expression Evidence Scores	1.0	0.23362
GSE129244_3_v_5_lmo2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
intermediate stratum of SePal	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.30611
JHH6	CCLE Cell Line Gene CNV Profiles	-1.0	-1.54411
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.24946
Primary somatosensory area, upper limb, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.1608
FOXM1	ChEA Transcription Factor Targets	1.0	null
H3K27ac_bone marrow_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
regulation of cell communication	GO Biological Process Annotations 2015	1.0	null
Perturb_10699_KD_CD274_SRP307356	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.52438
Perturb_7416_KD_METTL14_SRP040278	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	11.7577
H3ac_C2C12_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Neuroblastoma	DisGeNET Gene-Disease Associations	1.0	null
Perturb_394_KO_FOXM1_SRP272209	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.67893
GTEX-N7MS-0011-R1a-SM-2HMJG	GTEx Tissue Sample Gene Expression Profiles	1.0	0.84024
GSE202434,GSE202438_3_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
ZEB1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_GM12864_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8972_KD_RBL1_SRP218370	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.06797
H3K4me1_placenta_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7762_KD_IER3_SRP348787	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.39719
reticular formation of p2Lim	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.00514
MTA3_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_Adult Kidney	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
outer SZ in dorsolateral prefrontal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.01047
Omegasome	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.689
Lung squamous cell carcinoma_LUSC_TCGA-85-A4CN-01A-11R-A24H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Ovarian cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.559
H3K4me3_kidney epithelial cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
TPGS1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.53715
HMGN3_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ovary	GTEx Tissue Gene Expression Profiles	-1.0	-0.969688
TEAD4	ChEA Transcription Factor Targets	1.0	null
GSE188458_2_v_1_hydrogen peroxide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
19841744-TableS5	GeneSigDB Published Gene Signatures	1.0	null
Perturb_15423_KD_PXN_SRP199368	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.7932
Perturb_8092_KD_PUF60_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE153867_6_v_4_olaparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me1_mammary epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
SARS-CoV MA15_Day4_None_GSE49262	GEO Signatures of Differentially Expressed Genes for Viral Infections	1.0	1.98069
PMC4387713-supp_gad.255984.114_Table_S5.xlsx-S5E-Down_H3K27me3_DPY30_KD-Unnamed_12_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_8785_KO_HNF6_SRP217514	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.341
Perturb_7587_KO_ALKBH5/FTO_SRP362871	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.2411
GSE215086_4_v_7_batf_human	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC13127299-mmc2.xlsx-PBX1_kdRNAseq-hgnc_symbol_PBX1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_692_KO|KD_CD33|PTPN6_SRP275597	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.41721
Perturb_735_KD_PAF1_SRP048744	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.00236
GSE123105,GSE124556_0_v_2_pcf11_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_14321_KD_CD95L_SRP111532	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Taenia tecta, ventral part, layer 2	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.18888
amygdaloid complex_12 pcw_F_13060	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.896148
OB outer plexiform layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.09123
REST_Panc1_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2705_KD_HOXA11_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.8779
GSE178340_1_v_2_carfilzomib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC10082806-42003_2023_4756_MOESM4_ESM.xlsx-AML2_RelvsTum_DMRs_anno-annot_symbol_RUNX3	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_9963_KD_MTPAP_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.89337
Perturb_3589_KO_DDX6_ERP024006	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.82566
H3K4me3_CH12.LX_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_11971_KO_SUZ12_SRP327198	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.50956
CTCF_A549_hg19_9	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Medulloblastoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.0
JUND_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TRIM59	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.10601
cytoplasm	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
GSE102505_4_v_2_tunicamycin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Lung squamous cell carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.22
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.11355
Perturb_17550_KD_HMG20A_SRP354496	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.56331
H3K27ac_ES-Bruce4_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
SNU46	DepMap CRISPR Gene Dependency	1.0	6.31048
HuCCT-1 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.196
SKN3	DepMap CRISPR Gene Dependency	1.0	2.1763
EZH2_myotube_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_erythroblast_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_GM13976_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_10109_KD_EIF4B_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.57264
HDAC1	ENCODE Transcription Factor Targets	1.0	null
PANC 04.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.07305
Perturb_7854_KD_CCNF/E2F7/E2F8_SRP212181	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.85386
Platelet alpha granule membrane	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.511
8229_SNRPD2_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	-1.0	-0.534956
Perturb_15476_OE_MYC_SRP218384	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.8447
Perturb_2430_KD_HOXA11_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.45755
Anterolateral visual area, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.12984
NCI-H1781	COSMIC Cell Line Gene Mutation Profiles	1.0	null
FOXK2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9548
SIRT6_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE147366_3_v_2_med13_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_3194_KO_SE12313b_SRP266195	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE174735_4_v_3_il22_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-VS-A8EH-01A-11R-A36F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_14315_KO_PDE10A_SRP300922	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.61092
Perturb_12296_KD_RORC_SRP066204	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-19.699
ETS1_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PE/CA-PJ15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.11355
Perturb_2331_KD_SNRPB_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.63401
GSE160246_0_v_1_cpeb4_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE226249_0_v_1_pirfenidone_human	RummaGEO Drug Perturbation Signatures	1.0	null
Buccal mucosa	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.796
MYBL1-21750041-SPERMATOCYTES-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
gastric	GeneRIF Biological Term Annotations	1.0	null
GSE139540_0_v_2_menadione_human	RummaGEO Drug Perturbation Signatures	-1.0	null
YY1_K562_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H2AK5ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
zfpm2_19411579_heart_lof_mouse_gpl1261_gds3659	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.134184
Perturb_4853_KD_NKX25_SRP059197	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-15.9874
MYC_K562_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
tonsil_8b1	HPA Tissue Sample Gene Expression Profiles	1.0	0.875179
Perturb_8076_KD_AGO1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.60281
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.990528
BxPC-3	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-4.20565
FOXI1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.9281
Perturb_7748_KD_HRSP12_SRP155278	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.70414
TSEN2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.60115
CTCF_keratinocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TAF1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Disease of cellular proliferation	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	2.11
GTEX-PWO3-0926-SM-2I5EY	GTEx Tissue Sample Gene Expression Profiles	1.0	1.00546
GSE224096_1_v_0_cocaine_human	RummaGEO Drug Perturbation Signatures	-1.0	null
CAPAN-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.09773
CTCF_fibroblast of pulmonary artery_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_fibroblast of upper leg skin_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE158834_10_v_4_palm_human	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_8885_KD_FOXM1_ERP109084	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_9940_KD_MAK16_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.57195
GSE112860_3_v_4_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
CCNT2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE123943_1_v_3_sox1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_8494_KD_U2AF1_SRP221683	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.132
Lung squamous cell carcinoma_LUSC_TCGA-34-2596-01A-01R-0851-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Lung adenocarcinoma_LUAD_TCGA-05-5428-01A-01R-1628-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Bipolar disorder	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.539794
Skin Cutaneous Melanoma_SKCM_TCGA-EE-A2M8-06A-12R-A18S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CDX4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.76
Kidney renal papillary cell carcinoma_KIRP_TCGA-G7-A8LD-01A-11R-A36F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_9938_KD_DKC1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.5306
CAL-85-1	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
Perturb_5611_OE_Tpm4_SRP346384	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-20.0
H3K4me3_bronchial epithelial cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_2919_KD_Obf1_SRP237554	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.51891
Perturb_7363_OE_RBFOX1_SRP307800	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.7891
EP300	ENCODE Transcription Factor Targets	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-DQ-7589-01A-11R-2232-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CardiacMyocytes	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-2.298
POLR2A_MEL cell line_mm9_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HCC1599	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	1.27897
Perturb_7487_KD_SUPT4H1_SRP166802	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.59721
Upper respiratory tract disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.121
Perturb_13921_KO_PPARGC1A_SRP314654	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.94771
Malignant Tumor Of Cervix	DisGeNET Gene-Disease Associations	1.0	null
Perturb_11907_OE_Tlr7_SRP155370	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	15.4997
GSE104022_3_v_7_tamoxifen_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_14500_KD_RUNX1_SRP265128	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.34576
Perturb_505_KD_WTAP_SRP039397	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.34716
Perturb_8089_KD_HNRNPA2B1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.4376
Bed nuclei of the stria terminalis, anterior division, anteromedial area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.49659
H2AFZ_fibroblast of lung_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Mesothelioma_MESO_TCGA-LK-A4O0-01A-11R-A34F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2313_KD_LUC7L2_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.4145
FLI1-21571218-MEGAKARYOCYTES-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
GSE89018_10_v_8_cry2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
inferolateral temporal cortex (area TEv, area 20)_3 yrs_F_12836	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.42415
Urinary bladder cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.513
TSKU	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.47609
Perturb_2316_KD_PRPF31_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.55095
CBX3_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_17148_KO_H1_SRP076475	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.8456
MAX_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
YY1_SK-N-SH_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
cation binding	GO Molecular Function Annotations 2015	1.0	null
GTEX-NL4W-0011-R5a-SM-2I3GD	GTEx Tissue Sample Gene Expression Profiles	1.0	1.51158
Perturb_17537_KO_MAPK7_SRP265870	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.45068
pathways	GeneRIF Biological Term Annotations	1.0	null
GSE218580_1_v_5_fentanyl_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
parvocellular part of the r9LRt	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.28742
H3K9me3_A549_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
hsa-miR-148a-3p	MiRTarBase microRNA Targets	1.0	null
A-549 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.427
Artery - Tibial	GTEx Tissue Gene Expression Profiles 2023	-1.0	-0.667404
GSE146074_1_v_7_ly6e_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CTNNB_Activation (deltaNB-cateninER transgenics)_GDS1560_768_mouse_Skin - 7 Day	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GTEX-QDT8-0011-R2A-SM-32PKQ	GTEx Tissue Sample Gene Expression Profiles	1.0	1.54792
GTEX-N7MT-0011-R10A-SM-2I3E1	GTEx Tissue Sample Gene Expression Profiles	1.0	0.867515
Perturb_2074_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.3026
POLR2AphosphoS5_endothelial cell of umbilical vein_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27ac_HepG2_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE77108_0_v_1_saha_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE202434,GSE202438_9_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-22-4599-01A-01R-1443-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_6685_KD_SMARCA2_SRP378606	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_7180_KO_TrEx_SRP163035	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.6624
GSE137144_5_v_7_nlrp3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_H1 Derived Neuronal Progenitor Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_7837_KO_AGO1_SRP136692	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.51609
GSE185944_5_v_3_pth1r_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Bone marrow disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.075
ONECUT3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	173.523
GSE198165,GSE198166_6_v_2_zfp266_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Sarcoma_SARC_TCGA-SI-A71Q-01A-12R-A33J-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
A-2780 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.707
Perturb_10211_KD_TP63_SRP353945	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.6049
intermediate stratum of PcPV	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.12301
A-CA-04-2009(H1N1)_0Hour_23935999_GSE47962	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.58218
Perturb_15176_KD_CDH3_SRP366922	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.32548
Perturb_8894_KD_YAP1/WWTR1_SRP151027	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.78428
gracile nucleus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.997307
HIPK1_knockout_170_GSE39253	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	1.0	1.43993
H3K4me3_foreskin fibroblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_HepG2_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_11389_KD_BRG1_SRP261084	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.46974
Perturb_8763_KD_ROBO1_SRP158939	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.87741
ARID3A_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_megakaryocyte_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-QVJO-0126-SM-3GIK4	GTEx Tissue Sample Gene Expression Profiles	1.0	1.21063
Bladder Neoplasm	DisGeNET Gene-Disease Associations	1.0	null
Lingula (I)	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.47413
Lung squamous cell carcinoma_LUSC_TCGA-60-2722-01A-01R-0851-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Penfluridol_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0192055
UBXN6	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.20633
Perturb_8125_KD_LARP4_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.07604
GLYATL1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.01632
CHD1_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Ocular cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.038
globus pallidus, external segment, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.65196
H3K4me1_HepG2_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_HCT116_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GATA1	ENCODE Transcription Factor Targets	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-6010-01A-11R-1686-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_mammary epithelial cell_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC5651844-41467_2017_1173_MOESM4_ESM.xlsx-sheet_1-Supplementary_Data_1_Down_regulated_genes_in_YEATS2_KD_cells_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_15867_KD_KDM3A_SRP248023	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_4301_KO_Serpine1_SRP179032	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	1.30422
parasolitary nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.32397
SKIL	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.52575
GSE231648_0_v_3_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_bone marrow_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K9ac_H1-hESC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-QMR6-1926-SM-32PL9	GTEx Tissue Sample Gene Expression Profiles	1.0	0.949706
PMC7405480__F2	PFOCR Pathway Figure Associations 2024	1.0	null
GSE114690_2_v_0_tnfsf14_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
TFCP2L1	ChEA Transcription Factor Targets	1.0	null
PMC7346435-12864_2020_6860_MOESM6_ESM.xlsx-H1_ZF_Oocyte_Specific-GeneH_CREBZF	Rummagene Transcription Factor Associations 2026	1.0	null
NCI-H1651	COSMIC Cell Line Gene Mutation Profiles	1.0	null
H3K27ac_IMR90	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
H3K36me3_MEL cell line_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-66-2770-01A-01R-0851-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HCC95	CCLE Cell Line Gene Expression Profiles	1.0	1.88773
A-VN-1203-2004(H5N1)_Day7-10^2pfu_22074594_GSE33263	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.97898
PMC7773022__F9	PFOCR Pathway Figure Associations 2023	1.0	null
GSE180641_0_v_1_zfp503_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
TCF7L2	ENCODE Transcription Factor Targets	1.0	null
GSE202825_2_v_1_ano1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
rostral migratory stream	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.885347
Lung adenocarcinoma_LUAD_TCGA-38-4630-01A-01R-1206-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HEL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.10386
heart_6b	HPA Tissue Sample Gene Expression Profiles	-1.0	-1.20277
Perturb_15166_KO_ZAP_SRP288333	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.15389
PMC9574515-mmc2.xls-THP1_0_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
GSE255680_1_v_3_igf2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PAX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9993
GSE139540_4_v_1_menadione_human	RummaGEO Drug Perturbation Signatures	1.0	null
MXI1_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-R55F-1226-SM-2TF59	GTEx Tissue Sample Gene Expression Profiles	1.0	1.21254
NCI-H23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.866753
Kidney renal clear cell carcinoma_KIRC_TCGA-CZ-5469-01A-01R-1503-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
POLR2A_bone marrow macrophage_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Bile duct carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.434
X	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.827031
POLR2A_A549_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CHD2_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NFIC_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MAX_ECC-1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Generalized seizures_Brain_GSE6614	GEO Signatures of Differentially Expressed Genes for Diseases	-1.0	-1.70245
GSE202434,GSE202438_13_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
SK-N-SH cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.89
GSE119978,GSE180930_6_v_8_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
COCM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	1.0	null
KDM1A	ENCODE Transcription Factor Targets	1.0	null
ubiquitination	GeneRIF Biological Term Annotations	1.0	null
RCOR1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CEBPB	ENCODE Transcription Factor Targets	1.0	null
bed nucleus of the stria terminalis, laterocentral division	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.63221
r7 part of the dorsal cochlear nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.13604
GTEX-UJHI-0726-SM-3DB92	GTEx Tissue Sample Gene Expression Profiles	1.0	0.925138
Perturb_5996_KD_BCLAF1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
retina	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-0.867135
Perturb_14119_KD_RPS6KB2_SRP187713	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.70234
GSE211177,GSE211178_4_v_10_ets1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_6404_KO_ERBB_SRP118937	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
orbital frontal cortex_13 pcw_M_12888	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.866237
Perturb_5395_KD_LIM1_SRP402415	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.29876
GSE221004_3_v_0_prdm6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Childhood Osteosarcoma	DisGeNET Gene-Disease Associations	1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_8 yrs_M_12841	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.2027
Perturb_12950_KO_MEN1_SRP222871	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.77603
GSE158834_7_v_4_palmitic acid_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_2835_KD_FOXA1_SRP313175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE203362_0_v_1_enzalutamide_human	RummaGEO Drug Perturbation Signatures	1.0	null
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-C5-A2M2-01A-21R-A18M-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
FOXM1-26456572-MCF-7-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
H3K4me3_fibroblast of villous mesenchyme_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
MELHO	DepMap CRISPR Gene Dependency	1.0	2.50702
CHD4	ENCODE Transcription Factor Targets	1.0	null
Connective tissue	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
GSE137914_4_v_5_tet3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Genetic disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.244
H3K4me3_erythroblast_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
PMC10175786-Table4.XLSX-Sheet_1-GSE7410_AND_GSE63514_NOT_GSE9750_NOT_Ferrotosis_genes_NR4A2	Rummagene Transcription Factor Associations 2026	1.0	null
MYC-19079543-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
Perturb_15191_OE_SOX5_SRP091936	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-19.1549
ESR1	Pathway Commons Protein-Protein Interactions	1.0	null
GSE231720,GSE231724_3_v_0_setd2_human	RummaGEO Gene Perturbation Signatures	1.0	null
PMC5193459-pone.0168968.s009.xlsx-Dharmacon_OTP_siRNA_Area-Symbol_OTP	Rummagene Transcription Factor Associations 2026	1.0	null
abnormal inner cell mass morphology	MGI Mouse Phenotype Associations 2023	1.0	null
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	3.19217
COLO 741	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-2.09645
zona incerta, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.18499
Perturb_12729_KD_INCA1_SRP221667	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.01766
MTA3_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE178340_1_v_3_carfilzomib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Adrenocortical carcinoma_ACC_TCGA-OR-A5KO-01A-11R-A29S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
UACC893	DepMap CRISPR Gene Dependency	1.0	10.7525
Acute myeloid leukemia	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.057
H3K4me3_cardiac muscle cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
TK-10	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.36658
GSE129389_0_v_4_tropifexor_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Anteroventral periventricular nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07282
CTCF_fibroblast of skin of abdomen_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-600	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.7397
POLR2A_K562_hg19_9	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Colonic disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.241
Craniofacial Abnormalities	CTD Gene-Disease Associations	1.0	1.01814
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	43.8696
GSE242199_6_v_3_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_3964_KO_KFL5_SRP254802	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.51727
GSE223008_7_v_1_calhm6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
ELF1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_7568_KD_CPSF6_SRP327319	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.95336
Myeloid neoplasm	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.082
LUDLU1	CCLE Cell Line Gene CNV Profiles	1.0	1.35166
POLR2A_K562_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Adrenocortical carcinoma_ACC_TCGA-OR-A5J7-01A-11R-A29S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
embryonic lethality, complete penetrance	MGI Mouse Phenotype Associations 2023	1.0	null
PMC8528285-pbio.3001085.s010.xlsx-Fig_S7A-GENE_LIST_UPLOADED_TO_ENRICHR_MLX_TESTES_855_GENES_MLX	Rummagene Transcription Factor Associations 2026	1.0	null
GSE85880,GSE85881_0_v_2_tretinoin_human	RummaGEO Drug Perturbation Signatures	1.0	null
COLO 794	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.874618
GATA3-21878914-MCF-7-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_8186_KD_DNAJC21_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.3994
Perturb_8804_KD_PTB_SRP069229	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.60377
anterior (rostral) cingulate (medial prefrontal) cortex_30 yrs_F_12290	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.10637
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-DS-A0VL-01A-21R-A10U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Reflex, Abnormal	CTD Gene-Disease Associations	1.0	1.4591
SBC-3	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-3.72413
GSE130383_1_v_0_gps2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE240386,GSE242143_1_v_4_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_9885_KD_HNRNPL_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.99143
subparafascicular nucleus of thalamus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.78166
Perturb_5405_KD_RORB_SRP348097	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.33609
Perturb_15717_OE_Ctcf_SRP173291	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	1.72711
DOHH-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.21919
Brain Lower Grade Glioma_LGG_TCGA-HT-7467-01A-11R-2027-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
BHLHE40_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_fibroblast of dermis_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_14572_KO_EP300_SRP336466	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.10247
Adult Medulloblastoma	DisGeNET Gene-Disease Associations	1.0	null
GSE142684_0_v_5_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
VI, right, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.38199
Perturb_15168_KO_ZAP_SRP288333	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.22043
H2AFZ_CD14-positive monocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	2.075
c-Myc_OE_GDS3321_157_mouse_lung adenocarcinomas alveolar epithelia	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GSE202434,GSE202438_6_v_0_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_6104_OE_WSTF_SRP400122	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.74983
SP1_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
A-427	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.22782
Bladder Urothelial Carcinoma_BLCA_TCGA-G2-A2EF-01A-12R-A18C-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
testis_7d	HPA Tissue Sample Gene Expression Profiles	1.0	0.844078
H3K4me1_CH12.LX_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7644_KD_METTL3_SRP154311	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.31269
GABPA_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8215_KD_SUB1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.4418
Interstitial cell of Cajal	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.038
GTEX-QVUS-0226-SM-3GIJY	GTEx Tissue Sample Gene Expression Profiles	1.0	1.01079
GSE248045,GSE248046_4_v_2_runx1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
TCF12_ECC-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CREB1_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Endocrine system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.659
BCL11A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6915
hsa-miR-4511	TargetScan Predicted Conserved microRNA Targets	1.0	0.49473
Perturb_8799_OE_HOTAIR_SRP352837	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.04087
GTEX-QMR6-0011-R2A-SM-32PKV	GTEx Tissue Sample Gene Expression Profiles	1.0	1.44958
Perturb_4931_OE_KLF17_ERP131959	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.19487
H3K4me3_brain microvascular endothelial cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_MCF-7_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_4758_KO_DLG2_SRP315088	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.92548
Bone marrow cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.08
PMC10709143-41556_2023_1271_MOESM9_ESM.xls-Up_in_PAX7--Target_name_PAX7	Rummagene Transcription Factor Associations 2026	1.0	null
2313287	DepMap CRISPR Gene Dependency	1.0	2.4152
Perturb_14570_KO_RORC_SRP185849	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.88298
POLR2AphosphoS5_G1E_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE134191_3_v_5_metformin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-B4-5832-01A-11R-1672-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
BCL3_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC5013636-ncomms12601-s5.xlsx-TCF3-Groups_TCF3	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_7750_KD_POP1_SRP155278	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.73396
GSE121198,GSE129782_1_v_0_arid1a_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE112760,GSE112767_1_v_3_ddx6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CHD2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE140651,GSE140653_2_v_1_med1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GTEX-PWO3-0011-R3A-SM-2I5EX	GTEx Tissue Sample Gene Expression Profiles	1.0	0.896902
SZ in medial temporal-occipital cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.44782
Perturb_15871_KO_PAX3/FOXO1_SRP293781	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.52241
Perturb_485_KO_ITGB1_SRP320563	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.89084
urogenital system	TISSUES Experimental Tissue Protein Expression Evidence Scores	1.0	0.23362
transition metal ion binding	GO Molecular Function Annotations 2015	1.0	null
Perturb_9676_KO_C9orf72_SRP242090	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.79338
Brain Lower Grade Glioma_LGG_TCGA-DB-A64U-01A-11R-A29R-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE166783_3_v_2_tp53_human	RummaGEO Gene Perturbation Signatures	-1.0	null
15474998-tableS1b	GeneSigDB Published Gene Signatures	1.0	null
nucleus	LOCATE Predicted Protein Localization Annotations	1.0	null
Perturb_8277_KD_UTP18_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.89071
GSE230744,GSE237803_0_v_2_hira_human	RummaGEO Gene Perturbation Signatures	1.0	null
layer 1 of PCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.26893
SUP-B15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.55029
888	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.58421
Kidney renal clear cell carcinoma_KIRC_TCGA-BP-4989-01A-01R-1334-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
OLIG3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.4026
esr1_21713035_mcf7_lof_human_gpl570_gds4061	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-2.20486
Disease of anatomical entity	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	2.047
GSE144115_1_v_3_stag2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
intracellular part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma_DLBC_TCGA-FF-8041-01A-11R-2213-07	TCGA Signatures of Differentially Expressed Genes for Tumors	-1.0	null
GTEX-XMD1-0011-R8A-SM-4AT48	GTEx Tissue Sample Gene Expression Profiles	1.0	1.23491
GSE112762,GSE112767_2_v_3_dgcr8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_14176_KO_CD123_SRP387539	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.4927
Lung adenocarcinoma_LUAD_TCGA-55-1596-01A-01R-0946-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
membrane-bounded organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
NR4A2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2552
ZC3H11A_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Lymphatic system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.256
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	1.79425
primary motor-sensory cortex (samples)_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	2.01559
H3K4me1_Adult Liver	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
CTB-1	COSMIC Cell Line Gene Mutation Profiles	1.0	null
COR-L279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.11355
Skin Cutaneous Melanoma_SKCM_TCGA-EE-A2A0-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC10794847-mmc6.xlsx-PIAS1_KD_down-Table_S5_Genes_differentially_expressed_with_PIAS1_knockdown_in_keratinocytes_cultured_in_the_differentiation_condition_Related_to_Figure_5_AR	Rummagene Transcription Factor Associations 2026	1.0	null
hsa-miR-424	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
Perturb_2362_KD_ZNF581_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	15.1404
PMC5245798-pgen.1006538.s023.xlsx-Sheet1-HOXA2_HOXA2	Rummagene Transcription Factor Associations 2026	1.0	null
Alcohol use disorder (total score)	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.769897
SOX13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.3888
Perturb_12315_KO_AGO1_SRP136692	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
molecular_function	GO Molecular Function Annotations 2015	1.0	null
GSE188870,GSE188871_0_v_5_kat7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE190555,GSE190557_2_v_0_chd4_human	RummaGEO Gene Perturbation Signatures	-1.0	null
ventral part of JcP	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.09098
Perturb_8868_KD_PNN_SRP063860	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.08723
GSE158715_3_v_0_cyp1b1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
U266B1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.970956
TEAD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	37.6293
PMC5013636-ncomms12601-s5.xlsx-SP1-Groups_SP1	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me3_Skeletal Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CV-7254-01A-11R-2016-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
NCIH1693	CCLE Cell Line Gene Expression Profiles	1.0	1.38445
GSE210225_0_v_1_uba6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE157282_0_v_1_doxorubicin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K27ac_H1 BMP4 Derived Trophoblast Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_7380_KO_SMG7_ERP122822	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.74512
GSE206270_2_v_0_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE100102_2_v_5_cgas_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.50888
CBX3	ENCODE Transcription Factor Targets	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CR-5243-01A-01R-1514-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Squamous cell carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.471
Lung adenocarcinoma_LUAD_TCGA-75-6214-01A-41R-1949-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Entecavir (monohydrate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0186713
POLR2AphosphoS5_G1E-ER4_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_13680_KD_KDM3B_SRP221048	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.64325
Carcinoma	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
OVCA 432	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.98201
SREBP-SCAP-Insig complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.62
POU5F1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.3977
Perturb_8109_KD_MSI2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.39586
GSE186810,GSE186813_7_v_0_furin_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Biliary tract disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.324
Perturb_7286_KD_HNRNPG_SRP064870	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.69026
Perturb_7403_KD_HNRNPA2B1_SRP010280	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.98134
HS 766T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00206
ACHN	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.09454
Perturb_8840_KO_AKIRIN2_SRP281428	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.86549
NFIA_Deficiency_GDS2775_640_mouse_Postnatal brains (at P16)	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
GSE154464_1_v_2_cdk6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Viral infectious disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.48
Lung squamous cell carcinoma_LUSC_TCGA-98-A53I-01A-31R-A262-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
KLF4-18555785-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
GSE180185_4_v_1_setbp1_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE184892_7_v_5_trehalose_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE86813,GSE86814_0_v_1_atf7ip_human	RummaGEO Gene Perturbation Signatures	1.0	null
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.11355
Perturb_18453_KO_LTR7YB_SRP194102	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.95687
Perturb_8138_KD_IGF2BP2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-15.5868
H3K4me1_astrocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE198165,GSE198166_5_v_11_zfp266_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE142210_4_v_5_panobinostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
inner SZ in orbital frontal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.989294
Perturb_688_KD_ASAP2_SRP406127	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
ZNF274	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.6032
Head and neck squamous cell carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.002
CTCF_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POLR2AphosphoS5_endothelial cell of umbilical vein_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE195503_3_v_0_progesterone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
SPI1_GM12891_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Disease of metabolism	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.12
H3K4me3_bone marrow macrophage_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8491_KD_CGA/UCG_SRP119324	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.16707
hippocampus (hippocampal formation)_4 mos_M_12296	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.90305
NCI-H1299	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.35875
Perturb_12742_KD_GOT1_SRP282058	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.67511
H3K4me1_Brain Mid Frontal Lobe	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Colo-201 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.763
GSE226285_3_v_0_glutathione_human	RummaGEO Drug Perturbation Signatures	-1.0	null
TLX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.2022
GSE131649_4_v_7_hemin_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE210580_5_v_7_rag2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H3K4me3_BE2C_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_5661_KO_ID2_SRP336141	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-19.0969
H3K4me3_fibroblast of lung_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_5548_KD_ASC_SRP310464	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.51374
U266B1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.07059
organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
orbital frontal cortex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.36944
MAX_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8841_KO_PSMA3_SRP281428	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-18.1611
H3K4me3_brain microvascular endothelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_G1E_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE174735_1_v_3_il22_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H3K4me3_cardiac fibroblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE241701_1_v_0_daxx_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
ESR1_KD_GDS4061_453_human_MCF7 breast cancer cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
Oc cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.944
small embryonic epiblast	MGI Mouse Phenotype Associations 2023	1.0	null
ETS1_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE117042_1_v_3_tunicamycin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Cerebral cavernous malformation	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.062
Pancreatic carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.101
PTBP1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.11164
FOXM1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE242199_2_v_0_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
TCF3	ENCODE Transcription Factor Targets	1.0	null
Acute Kidney Injury	CTD Gene-Disease Associations	1.0	1.02299
Perturb_7321_KD_METTL14_SRP064870	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	11.7577
mantle zone of r7Co	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.12832
Lung adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.408
GSE77108_6_v_1_saha_human	RummaGEO Drug Perturbation Signatures	1.0	null
BRCA1	ENCODE Transcription Factor Targets	1.0	null
GSE231648_4_v_2_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NCI-H460	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00206
PMC9583506__F2	PFOCR Pathway Figure Associations 2024	1.0	null
PMC7782476-41467_2020_20434_MOESM7_ESM.xlsx-KLF14_string_interactions-node2_KLF14	Rummagene Transcription Factor Associations 2026	1.0	null
POLR2A_ES-Bruce4_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27ac_liver_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
GSE165334_3_v_1_dabrafenib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_2431_KD_IRX6_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.45944
globose nucleus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.84073
CTCF_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3915_KD_CTNNB1_DRP003300	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.06137
Perturb_13868_KD_KDM6B_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE233679_12_v_7_nicotinamide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE208254_4_v_5_irf8_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
NCIH226	DepMap CRISPR Gene Dependency	1.0	2.18247
Perturb_12572_KD_MSI1_ERP124202	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.95181
GSE226091,GSE226092_0_v_4_sall1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Brain Lower Grade Glioma_LGG_TCGA-DU-5854-01A-11R-1708-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Intrinsic epigenetic age acceleration	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.869897
GSE226249_0_v_4_pirfenidone_human	RummaGEO Drug Perturbation Signatures	1.0	null
POLR2A	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.04244
VZ in posteror frontal cortex (motor cortex)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.53664
H3K4me3_retinal pigment epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Respiratory system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.944
CTCF_fibroblast of dermis_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_1160_KD_CELSR2_SRP149837	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.58229
Perturb_9281_KO_HNRNPUL1_SRP374878	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.5045
GSE242199_9_v_5_ntrk2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
WHSC1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Eca-109 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.998
H3K4me3_Mobilized CD34 Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE180185_4_v_8_setbp1_human	RummaGEO Gene Perturbation Signatures	1.0	null
20937356-TableS2	GeneSigDB Published Gene Signatures	1.0	null
Perturb_16954_KO_MLX_SRP183152	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.27261
striatum_24 pcw_M_12288	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.904653
inferolateral temporal cortex (area TEv, area 20)_36 yrs_M_12302	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.0697
Perturb_6463_OE_NFAT1_SRP173011	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	18.8861
GSE111138,GSE111149_1_v_0_runx3_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
21205295-TableS1	GeneSigDB Published Gene Signatures	1.0	null
interacts	GeneRIF Biological Term Annotations	1.0	null
Perturb_8080_KD_DDX24_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.64505
GSE195513_0_v_3_cpeb1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
innate	GeneRIF Biological Term Annotations	1.0	null
RFX5_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15386_KD_FGFRL1_SRP319157	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.7525
Perturb_6081_KD_TRA2A_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_5660_KO_ID2_SRP336141	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.86006
PMC11743796-41420_2025_2295_MOESM5_ESM.xlsx-aged_LPS_BV-2_vs_human_downreg-human_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
ctnnb1_19652203_myeloma_lof_human_gpl570_gds3578	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.049265
GSE168697_0_v_1_wdr6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Panc1_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE233647_4_v_6_docetaxel_human	RummaGEO Drug Perturbation Signatures	1.0	null
PMC3355086-pgen.1002728.s003.xlsx-Tabelle1-HEY1_downregulated_HEY1	Rummagene Transcription Factor Associations 2026	1.0	null
PMC12048643-44318_2025_409_MOESM3_ESM.xlsx-regulonTargets-CTCF_CTCF	Rummagene Transcription Factor Associations 2026	1.0	null
GTF2B_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_13603_KD_KLF4_SRP221596	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
CAL-39	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
Perturb_8127_KD_ASCC1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.0375
GSE246461,GSE246463_5_v_0_mecp2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
dorsolateral prefrontal cortex_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.47816
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-8_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
Lingula (I), molecular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.64234
H3K27ac_spleen_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
binding	GO Molecular Function Annotations 2015	1.0	null
GSE197630_1_v_0_enzalutamide_human	RummaGEO Drug Perturbation Signatures	1.0	null
KDM5B	ChEA Transcription Factor Targets	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-MZ-A6I9-01A-11R-A31N-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GTEX-T6MN-0011-R1A-SM-32QOY	GTEx Tissue Sample Gene Expression Profiles	1.0	1.33624
Perturb_9944_KD_RBM15_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	11.9954
serve	GeneRIF Biological Term Annotations	1.0	null
CHL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.869532
NCI-H1734	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.48573
KYSE-520	COSMIC Cell Line Gene Mutation Profiles	1.0	null
TEF-1	MotifMap Predicted Transcription Factor Targets	1.0	null
Perturb_8257_KD_RBM27_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.54881
GSE113734_3_v_0_qprt_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Breast Myoepithelial Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
CTCF_fibroblast of the aortic adventitia_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-B8-4143-01A-01R-1188-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC7672319-mmc3.xlsx-DREAM_MSigDB62-FISCHER_DREAM_TARGETS_KCNIP3	Rummagene Transcription Factor Associations 2026	1.0	null
Ventral posterolateral nucleus of the thalamus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.05801
Cognition Disorders	CTD Gene-Disease Associations	1.0	1.22274
H3K4me3_fibroblast of gingiva_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K9me3_mammary epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me1_thymus_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_A549_hg19_4	ENCODE Histone Modification Site Profiles	1.0	null
occipital pole, left, lateral aspect	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.61578
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	40.9387
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-2_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
Infralimbic area, layer 2	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.35305
UBC	Pathway Commons Protein-Protein Interactions	1.0	null
Large intestine cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.742
RXRA_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-77-7335-01A-11R-2045-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CEBPB_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PML_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2730_KD_BCL11A/MBNL1_SRP258724	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	13.7452
Lung adenocarcinoma_LUAD_TCGA-05-4250-01A-01R-1107-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K9ac_Duodenum Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
POLR2A_thymus_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE157555,GSE157556_4_v_2_foxa2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GTEX-PWO3-0011-R2A-SM-2S1OX	GTEx Tissue Sample Gene Expression Profiles	1.0	0.882077
Perturb_17201_OE_GATA3|JUN_SRP188712	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.60228
7608_RUVBL2_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.592324
cerebellar cortex_3 yrs_F_12836	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.17609
Perturb_16788_KD_ETS1_SRP131807	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.32975
2932_RIPOR1_P1	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.711966
GSE149903_5_v_2_myd88_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NCI-H1882	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.07054
Perturb_2317_KD_PRPF31_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.09246
GSE133927_1_v_3_meox1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_5657_KD_EF1_SRP201842	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-15.1282
Brain Lower Grade Glioma_LGG_TCGA-DU-5851-01A-13R-1896-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
u138mg	HPA Cell Line Gene Expression Profiles	-1.0	-0.937616
GSE169152_3_v_4_ibrutinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_13110_KO_Foxm1_SRP194062	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-9.2049
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.989634
Central nervous system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.451
H3K4me1_fibroblast of dermis_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE245407,GSE245412_0_v_1_smurf1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Striatum dorsal region	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.09167
brain	HPA Tissue Gene Expression Profiles	1.0	0.973955
NPC	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.855
Perturb_2373_KO_ASXL1_SRP305063	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.48062
EZH2_astrocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
C3A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.824668
Perturb_1368_KD_IGF2BP2_SRP252209	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.3064
MCF-10A cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.87
POLR2AphosphoS5_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
GSE179880_7_v_5_e2f4_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
hsa-miR-148a	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
Perturb_15437_KD_NUSAP1_SRP074246	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.70069
Perturb_9130_KD_PHGDH_ERP020769	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.72374
GSE246195,GSE246305_2_v_5_sin3a_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
NR2F2_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_12166_KO_TRAM2_SRP254106	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.87191
KIAA1586	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.02863
SIN3A_Panc1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6051_KD_PPHLN1_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE146074_0_v_3_ly6e_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PU.1_KD_GDS2411_175_mouse_Preleukemic hematopoietic stem cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
Malignant exocrine pancreas neoplasm	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.1
RCOR1_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE174522_1_v_0_spp1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Crus I, left, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.05865
Agranular insular area, dorsal part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.03735
M-1	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	1.0	1.6872
FOXA1-27270436-VCAP-HUMAN-PROSTATE-CARCINOMA	ChEA Transcription Factor Targets 2022	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-92-7340-01A-21R-2045-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_8226_KD_EWSR1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.68148
MAX_ECC-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC7206068__F3	PFOCR Pathway Figure Associations 2024	1.0	null
CTCF_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_cortical plate_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
MYC_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HDAC2	ENCODE Transcription Factor Targets	1.0	null
H3K56ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_2834_KD_ESR1_SRP313175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
SYNCRIP_OE_GDS3575_87_mouse_C57BL/6 mice	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
PHF8_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Diazinon	CTD Gene-Chemical Interactions	1.0	null
PTEN_KD_GDS4759_337_mouse_E16 primary cortical neuron cultures	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-D3-A2J8-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Liver hepatocellular carcinoma_LIHC_TCGA-G3-A25X-01A-11R-A16W-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
dorsal thalamus_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.08982
Perturb_2284_OE_TLX_SRP358206	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Pancreatic cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.44
zinc ion binding	GO Molecular Function Annotations 2015	1.0	null
Perturb_8164_KD_TARDBP_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-18.9586
GSE198165,GSE198166_6_v_11_zfp266_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE178255_3_v_4_tlr4_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE172295_1_v_2_sh3gl1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
TBL1XR1	ENCODE Transcription Factor Targets	1.0	null
H3K23me2_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Reproductive system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.8
H3K9ac_skeletal muscle myoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.91844
GSE249098_1_v_2_mthfd1l_human	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_16481_KO_IL6_SRP159090	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	15.8779
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-1_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
NFE2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MOR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00206
Perturb_13885_KD_CDK4/CDK6_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.5594
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-4727-01A-01R-1436-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
POLR2AphosphoS5_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
embryonic stem feeder layer	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	1.0	1.07419
KDM5B_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF384_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
15474998-tableS1c	GeneSigDB Published Gene Signatures	1.0	null
Perturb_8821_KD_TRRAP_SRP106050	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.567
IX	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.89996
intercalated nucleus of medulla	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.49807
REST_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PHF8	ENCODE Transcription Factor Targets	1.0	null
BRCA1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
POU4F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.1964
Perturb_8079_KD_DDX21_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.6784
Perturb_5896_KD_CCDC59_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.7472
Lung adenocarcinoma_LUAD_TCGA-38-4627-01A-01R-1206-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_8104_KD_CPSF7_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.01561
GSE171837_0_v_3_bortezomib_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_1198_KO_Klf16_SRP302435	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-4.65128
NR2F2	ENCODE Transcription Factor Targets	1.0	null
Norepinephrine (hydrochloride)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0325577
VZ in inferolateral temporal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.841179
TAF1_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_7738_KD_HRSP12/CNOT1_SRP155278	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.53439
RAD21_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_13495_KD_IGF2BP1_SRP291710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.05868
H3K27ac_embryonic fibroblast_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_HeLa-S3_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
GSE100316_5_v_2_mtor_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_15396_KD_CSN5_SRP316687	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.6198
Pi Mi complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.673
dorsal motor nucleus of the vagus (vagal nucleus)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.09115
H3K9ac_endothelial cell of umbilical vein_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K9me3_keratinocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-WZTO-0011-R7B-SM-4E3IS	GTEx Tissue Sample Gene Expression Profiles	1.0	1.72343
Non-Small Cell Lung Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
FOXC1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.8968
H3K4me3_CH12.LX_mm9_4	ENCODE Histone Modification Site Profiles	1.0	null
PMC9314667-Table_1.xlsx-Regulons-FOSL1_FOSL1	Rummagene Transcription Factor Associations 2026	1.0	null
H3K27ac_A549_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Gilin	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.536
upper limb region of M1	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.902272
TRIM28_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
16151515-TableS1	GeneSigDB Published Gene Signatures	1.0	null
MYC_MCF-7_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-QMR6-0011-R5A-SM-32PKT	GTEx Tissue Sample Gene Expression Profiles	1.0	0.922105
TFAP2A-35110662-HEPM-HUMAN-EMBRYO	ChEA Transcription Factor Targets 2022	1.0	null
GSE161170,GSE161268_1_v_3_med1_human	RummaGEO Gene Perturbation Signatures	1.0	null
H3K4me1_MEL cell line_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-DU-8167-01A-11R-2256-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
frhk4	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.732
Perturb_763_KD_SRRM2_SRP366559	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.40149
Perturb_8463_KO_IL10R2_ERP121014	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.58471
NCI-H358 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.645
hippocampus (hippocampal formation)_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.21878
H3K4me3_MCF-7_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
GSE149943_2_v_3_cd8a_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
USF1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
RERFGC1B	DepMap CRISPR Gene Dependency	1.0	2.37362
GTEX-XMD1-0011-R5A-SM-4AT47	GTEx Tissue Sample Gene Expression Profiles	1.0	0.878934
Perturb_2070_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.73137
GSE100316_3_v_4_mtor_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE132369,GSE132371_5_v_0_cccp_human	RummaGEO Drug Perturbation Signatures	-1.0	null
hsa-miR-548b-3p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.7397
Neoplasm Metastasis	CTD Gene-Disease Associations	1.0	1.052
red nucleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.03105
retrosplenial cortex	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.28598
Embryonic cerebral cortex	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.737
skeletal muscle	HPA Tissue Gene Expression Profiles	-1.0	-1.43699
SPCS2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.09017
H3K4me1_limb_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_4855_KD_ZNF503_SRP059197	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.78034
primary visual cortex (striate cortex, area V1/17)_10 mos_M_12977	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.13975
H3K79me2_MEL cell line_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_BJ_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
H3K9ac_GM12878_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
ZNF217	ENCODE Transcription Factor Targets	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-4735-01A-01R-1436-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Kidney renal papillary cell carcinoma_KIRP_TCGA-F9-A4JJ-01A-11R-A24Z-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
cell	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
GTEX-R55E-0011-R5A-SM-2TC5N	GTEx Tissue Sample Gene Expression Profiles	1.0	1.92487
PMC7614775-EMS178742-supplement-Proteomics_Table_1.pdf-213-ZNF276_ZNF276	Rummagene Transcription Factor Associations 2026	1.0	null
TAL1_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3848_KD_lncRNAAK096729_SRP192850	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
4943_MED20_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.501697
KLF4-18555785-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
GTEX-OHPN-0011-R5A-SM-2I5FF	GTEx Tissue Sample Gene Expression Profiles	1.0	0.930646
SW872	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-3.9055
SLC25A34	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.36036
Perturb_161_KO_Kdm4a_SRP192379	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	4.49819
496100380_FWM_no dementia_no TBI_78_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.40339
GSE140646_0_v_1_atf3_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE161295_0_v_5_cdk8_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC12494973-41467_2025_63880_MOESM1_ESM.pdf-176-RUNX2_RUNX2	Rummagene Transcription Factor Associations 2026	1.0	null
hypoglossal nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.02739
SIN3A_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-NPJ7-0011-R11A-SM-2I3E8	GTEx Tissue Sample Gene Expression Profiles	1.0	0.935607
indusium griseum	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.837587
H2AFZ_skeletal muscle myoblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Colorectal cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.577
CTCF_GM12864_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE195663_7_v_1_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_8495_KD_U2AF1_SRP221683	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.2794
GTEX-WL46-0011-R1A-SM-3LK6M	GTEx Tissue Sample Gene Expression Profiles	1.0	1.85128
UBTF_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
cell part	LOCATE Predicted Protein Localization Annotations	1.0	null
HCC1187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
Lung squamous cell carcinoma_LUSC_TCGA-22-5474-01A-01R-1635-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE164521_0_v_1_nitric oxide_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_7356_KO_NSUN6_SRP233222	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.49279
layer 1 of RSC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.02246
H3K4me3_placenta_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE112760,GSE112767_1_v_5_ddx6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE112762,GSE112767_1_v_3_dgcr8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_13853_KO_RET_ERP126468	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
496100537_FWM_no dementia_TBI_87_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.44081
POLR2A_HepG2_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-RU72-0011-R9A-SM-2TF67	GTEx Tissue Sample Gene Expression Profiles	1.0	0.981747
GSE233679_14_v_7_nicotinamide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_14237_KO_Tet1_SRP237910	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-20.0
CHD7	ENCODE Transcription Factor Targets	1.0	null
Adult respiratory distress syndrome	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.045
H3K4me3_fibroblast of lung_hg19_7	ENCODE Histone Modification Site Profiles	1.0	null
Pancreas	Roadmap Epigenomics Cell and Tissue Gene Expression Profiles	-1.0	-0.849425
superficial stratum of SeStr	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.58806
VZ in frontal polar cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.1269
Perturb_8492_KD_Mir34a_SRP133851	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
hsa-miR-3662	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.55165
H3K4me3_Adult Liver	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-6989-01A-11R-1915-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC8528285-pbio.3001085.s010.xlsx-Fig_S8E-GENE_LIST_UPLOADED_TO_ENRICHR_MNT_KO_3T3_ONLY_2084_GENES_MNT	Rummagene Transcription Factor Associations 2026	1.0	null
BHLHE23	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.9656
GSE180185_7_v_10_setbp1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GBX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.5807
E2F4_MCF 10A_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6435_KD_HOXA10AS_ERP131886	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	11.8535
H3K4me3_fibroblast of pulmonary artery_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
tRNA-intron endonuclease complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.551
PRDM1	JASPAR Predicted Transcription Factor Targets	1.0	null
GSE152246_0_v_1_dihydrotestosterone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Pancreatic adenocarcinoma_PAAD_TCGA-IB-7887-01A-11R-2156-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
TRIM17	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.05418
parolfactory gyri, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-2.43922
embryonic growth retardation	MGI Mouse Phenotype Associations 2023	1.0	null
VZ in primary visual cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.858138
GSE223008_9_v_8_calhm6_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE151829,GSE151831_1_v_0_aire_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
POLR2A_erythroblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00091
TAF1_PFSK-1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Bladder disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.492
YY1_NT2-D1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GATA1_G1E-ER4_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_686_KO_SLC15A4_SRP212091	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.31115
6135_PCNA_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.527377
CAMA1	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	1.0	0.658029
H3K4me3_cardiac fibroblast_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_brain microvascular endothelial cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal papillary cell carcinoma_KIRP_TCGA-BQ-5876-01A-11R-1592-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_GM12892_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Caudoputamen	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.09372
Perturb_334_KD_PHF10_SRP301562	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.31031
posterior (caudal) superior temporal cortex (area 22c)_13 yrs_F_12831	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.43396
Perturb_4339_OE_ISL1/LHX3_SRP271657	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.7634
DYNLRB1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.76234
10751_NON-TARGETING_NON-TARGETING	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.644566
TAF1_ECC-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-R55F-1526-SM-2TF4X	GTEx Tissue Sample Gene Expression Profiles	1.0	1.13678
Lung cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.953
PHOX2B-30127528-KELLY-HUMAN-BRAINNEUROBLASTOMA	ChEA Transcription Factor Targets 2022	1.0	null
hsa-miR-31	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.7397
Lung adenocarcinoma_LUAD_TCGA-38-4631-01A-01R-1755-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_8805_KD_PTB_SRP069229	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.26257
EP300_T47D_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
YY1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_7181_OE_MAGEA11_SRP216417	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.96666
CTCF_GM12878_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MYBL2	ENCODE Transcription Factor Targets	1.0	null
H3K4me2_skeletal muscle myoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
Perturb_7648_KD_METTL3_SRP154311	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.43242
Sarcoma_SARC_TCGA-X2-A95T-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Systolic blood pressure	GWAS Catalog SNP-Phenotype Associations 2025	1.0	1.21549
Perturb_12952_KO_ZFP36L2_SRP251843	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.577
GSE149903_5_v_7_myd88_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Bed nuclei of the stria terminalis, anterior division, fusiform nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.56649
sublayer 6b of OCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.11047
LUBAC complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.824
H3K4me3_mammary epithelial cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
bleomycin_mus musculus_gpl1261_gse25640	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
Sarcoma_SARC_TCGA-DX-A6YT-01A-21R-A355-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PANC1005	CCLE Cell Line Gene Expression Profiles	1.0	1.54182
PMC6987220-41467_2020_14312_MOESM5_ESM.xlsx-P53_Spheres-9_names_TP53	Rummagene Transcription Factor Associations 2026	1.0	null
GEO	COSMIC Cell Line Gene Mutation Profiles	1.0	null
DDX10	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.5935
SF268	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00091
CTCF_fibroblast of mammary gland_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_skeletal muscle myoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE88819_11_v_12_tug1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
TAF1_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K36me3_ES-Bruce4_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZSWIM7	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.0238
CTCF_fibroblast of gingiva_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-QDT8-0011-R1A-SM-32PKS	GTEx Tissue Sample Gene Expression Profiles	1.0	1.13908
Perturb_11688_KD_RRM2|CDKN2A_SRP212736	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.4627
Trimetrexate_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0198631
hsa-miR-3942-3p	TargetScan Predicted Conserved microRNA Targets	1.0	1.26663
Perturb_6071_KD_SLTM_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
FOXO6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.4995
lateral medullary reticular group, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.842205
POLR2AphosphoS5_PFSK-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
brain_3b	HPA Tissue Sample Gene Expression Profiles	1.0	0.849665
ARID3A_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
BCLAF1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Temsirolimus_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0226754
GTEx SmallIntestine 20-29 vs 50-59	GTEx Tissue-Specific Aging Signatures	-1.0	-5.34497
SCARA5_Down Expression_GSE32323_611_human_Colorectal Cancer Cell lines	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
testis_7a	HPA Tissue Sample Gene Expression Profiles	1.0	0.839648
PMC5263239-mmc2.xls-SEM_-_MLL-AF4-All_targets_genes_names_2597_unique_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
cSARS Bat SRBD_54Hour_None_GSE37827	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.20844
Pheochromocytoma and Paraganglioma_PCPG_TCGA-WB-A81M-01A-11R-A35L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
MYC-18358816-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
MAX_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me1_Peripheral Blood Mononuclear Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_14099_KD_AHR_SRP154013	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.11299
Perturb_452_OE_MYC_SRP171977	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE172247,GSE172250_0_v_2_mtor_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE132408_1_v_3_tet2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CR-7374-01A-11R-2016-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Primary immunodeficiency disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.095
YY1_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8221_KD_ACO1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.13098
GSE119978,GSE180930_0_v_7_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
TTK	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.06436
AN3CA	CCLE Cell Line Gene Expression Profiles	-1.0	-1.45531
SARS-dORF6_12Hour_23935999_GSE47960	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-3.11341
hsa-miR-761	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.24946
Sarcoma_SARC_TCGA-SI-A71O-06A-11R-A38C-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K27ac_Duodenum Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_13381_KO_CTIP2_SRP150394	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.48572
GSE111247_14_v_10_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
COLO 680N	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.24687
GSE189772,GSE189773_0_v_5_fbxo11_human	RummaGEO Gene Perturbation Signatures	1.0	null
GTEX-WL46-0011-R6A-SM-3LK6X	GTEx Tissue Sample Gene Expression Profiles	1.0	2.45379
Perturb_8241_KD_SRSF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	11.2673
SNU-216	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	1.0	null
hsa-miR-2909	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.40969
VZ in rostral cingulate neocortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.06206
Perturb_9402_KD_MYCN_SRP104120	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.04944
NCI-H82	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.66569
E2F4_myocyte_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15427_KD_RB1_SRP145071	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.93348
GSE113329,GSE113335_3_v_4_taf6l_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-BP-4964-01A-01R-1334-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC9235320-mmc2.xlsx-TableS12_MR-PheWAS-results-Supplementary_Table_12A_The_phenome-wide_Mendelian_randomization_results_for_the_6_prioritised_protein_targets_NR3C2	Rummagene Transcription Factor Associations 2026	1.0	null
ECSIT	Pathway Commons Protein-Protein Interactions	1.0	null
GSE252857_1_v_3_klf15_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H3K4me1_liver_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
WRNIP1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
EJM	DepMap CRISPR Gene Dependency	1.0	4.46562
Perturb_7599_KO_CTNNB1_ERP109990	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.68261
Retinal cell cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.097
MAX_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2719_KD_BRD_SRP115100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.32722
FOXA1-27270436-LNCAP-HUMAN-PROSTATE-CARCINOMA	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_6093_KD_ZC3H13_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_8185_KD_DNAJC2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.70296
layer 1 of OCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.1673
VIIIB, left, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.14167
regulation of intracellular signal transduction	GO Biological Process Annotations 2015	1.0	null
POLR2A_embryonic fibroblast_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
DICER1_KO_GDS4504_586_mouse_bone marrow granulocyte-macrophage progenitors	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
Perturb_6089_KD_YBX3_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE240386,GSE242143_1_v_6_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
Archenteron	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.596
hsa-miR-3150b-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
Perturb_8156_KD_FTO_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.19507
RBBP5_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
TCF12	ENCODE Transcription Factor Targets	1.0	null
POLR2A	ENCODE Transcription Factor Targets	1.0	null
hsa-miR-4790-3p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
GATA3_SH-SY5Y_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MXI1	ENCODE Transcription Factor Targets	1.0	null
H3K4me2_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Kidney Chromophobe_KICH_TCGA-KL-8336-01A-11R-2315-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Docetaxel_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0255442
Anterior cingulate area, dorsal part, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.61214
IRF1_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ELF1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE109285_3_v_2_glucagon_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_4471_KO_Prdm12_SRP334439	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	4.83693
GATA1_MEL cell line_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE171837_3_v_1_bortezomib_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE206270_2_v_3_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC11131031-pwad060_suppl_supplementary_tables_s3.xlsx-FOXO1-knockout_bulk_RNA-seq-Unnamed_1_FOXO1	Rummagene Transcription Factor Associations 2026	1.0	null
GSE142210_11_v_10_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
POLR2A_brain_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Disease by infectious agent	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.481
Prostate adenocarcinoma_PRAD_TCGA-HC-8216-01A-11R-A29R-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_8099_KD_UBE2L3_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.66431
PMC12623973-41467_2025_64981_MOESM3_ESM.xlsx-downregulated-c0_ACKR4_SCS_ceiling_LEC_TWIST1	Rummagene Transcription Factor Associations 2026	1.0	null
SIN3A_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9836_KD_GCN2_SRP248465	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.2186
H3K4me3_LNCaP clone FGC_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
palbociclib_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0282737
RKO	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.876676
POLR2A_GM12892_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_10218_KO_TNFAIP6_ERP126958	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.38453
estradiol_homo sapiens_gpl570_gds3283	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
PMC4390530-NIHMS667786-supplement-1.xlsx-Sheet1-Supplementary_Table_2_Genes_closest_to_AR_induced_ASH2L_peaks_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_13953_OE_lncNR2F1_SRP179994	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.69952
Taenia tecta	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.23327
Perturb_10001_KD_FMR1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.17813
Perturb_11666_KD_PTBP1_SRP113334	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.31028
MAZ_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Conventional (Clear Cell) Renal Cell Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
Perturb_8187_KD_HNRNPA1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.2982
Perturb_15447_KD_HDAC5_SRP273298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE121824,GSE121826_0_v_6_scaf8_human	RummaGEO Gene Perturbation Signatures	1.0	null
FOSL2_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-WL46-2926-SM-3LK82	GTEx Tissue Sample Gene Expression Profiles	1.0	1.44907
POFUT2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.08709
r3 pontine raphe nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.74308
EP300_SK-N-SH_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Liver hepatocellular carcinoma_LIHC_TCGA-DD-AA3A-01A-11R-A37K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE128844_0_v_2_chloroquine_human	RummaGEO Drug Perturbation Signatures	1.0	null
H3K4me3_cardiac mesoderm_hg19_7	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_599_OE_HOTAIR_SRP342161	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.0151
CNOT3-19339689-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
posteroventral (inferior) parietal cortex_10 mos_M_12977	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.35563
Head and Neck squamous cell carcinoma_HNSC_TCGA-CV-5978-01A-11R-1686-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-CH-5788-01A-11R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
H3K36me3_testis_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE123825_2_v_3_glud1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_8 yrs_M_12981	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.05767
GSE206870,GSE206872_4_v_2_ascl1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
BRCA1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.9723
GTEX-XMD1-0011-R9A-SM-4AT49	GTEx Tissue Sample Gene Expression Profiles	1.0	1.29853
PMC6433297-pbio.3000178.s012.xlsx-DREAM_targets-BUB1B_KCNIP3	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_3521_KD_FACT_SRP328843	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.28663
Perturb_6855_KD_YTHDF1_SRP287222	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.53043
GSE210580_3_v_11_rag2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE174498,GSE174500_5_v_1_asparaginase_human	RummaGEO Drug Perturbation Signatures	-1.0	null
NFIC::TLX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.5
PMC6151027-12864_2018_5080_MOESM3_ESM.xlsx-E16_vs_E20_814_AR-DEGs-Symbol_AR	Rummagene Transcription Factor Associations 2026	1.0	null
hydrocortisone_homo sapiens_keloid scar_gds3071	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
GSE192663_3_v_5_acly_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
hsa-miR-450b-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
Renal cell carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.231
Nodulus (X), granular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.13527
SW1783	CCLE Cell Line Gene CNV Profiles	-1.0	-2.03123
Perturb_474_KO_HDLBP_SRP261899	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.41961
GSE146074_0_v_7_ly6e_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
negative regulation of response to stimulus	GO Biological Process Annotations 2015	1.0	null
Ovarian Neoplasm	DisGeNET Gene-Disease Associations	1.0	null
Carcinoma Breast	DisGeNET Gene-Disease Associations	1.0	null
Phagophore assembly site membrane	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.544
H3255	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-2.06856
FOXP1	ChEA Transcription Factor Targets	1.0	null
GSE202434,GSE202438_2_v_5_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
GTEX-QVJO-0011-R4A-SM-2S1QL	GTEx Tissue Sample Gene Expression Profiles	1.0	0.981374
Retinoblastoma	DisGeNET Gene-Disease Associations	1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_13 pcw_M_12888	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.17128
PMC12005766-ADVS-12-2413120-s003.xlsx-VENN1-Table_S6_related_to_Figure_S6D_List_of_overlapping_DEGs_with_the_E3_or_DUB_gene_set_from_the_iUUCD_2_0_database_ZUP1	Rummagene Transcription Factor Associations 2026	1.0	null
EP300_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-T2IS-0011-R2A-SM-32QPF	GTEx Tissue Sample Gene Expression Profiles	1.0	1.83936
PFDN1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.87216
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.01829
GTEX-RVPV-0011-R3A-SM-2TF63	GTEx Tissue Sample Gene Expression Profiles	1.0	1.19287
NLRP3 inflammasome complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.493
STAT5A	ENCODE Transcription Factor Targets	1.0	null
Zinc finger, RING-type	InterPro Predicted Protein Domain Annotations	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-GV-A3JW-01A-11R-A20F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PRRX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.035
GSE91015_0_v_1_aire_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
medioventral part of putamen	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.52659
embryonic stem no feeder	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	1.0	0.879573
GTEX-WWYW-0011-R5A-SM-3NB3E	GTEx Tissue Sample Gene Expression Profiles	1.0	1.32159
NRF1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-1299	TargetScan Predicted Conserved microRNA Targets	1.0	0.119151
GATA3_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_6904_KD_OTX2_SRP347033	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE146074_1_v_8_ly6e_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Pulse pressure	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.769897
medial ganglionic eminence	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.79891
MYC_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3762_KO_TNFAIP3_SRP133440	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.00697
Carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.95
VPREB3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.0916
GSE202434,GSE202438_6_v_5_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
medial ganglionic eminence_9 pcw_M_12833	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	2.74025
Perturb_2718_KD_BRD_SRP115100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.90341
Perturb_7466_KD_ARIEL_SRP136083	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.22784
Perturb_11402_KD_CPT1A_SRP076884	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.78542
GSE153867_6_v_3_olaparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_6707_KD_ELOA_SRP314942	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.30867
hsa-miR-410	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.965816
Perturb_9818_KD_GATA3_SRP103740	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.32484
4950_MED27_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.501998
CESS	COSMIC Cell Line Gene Mutation Profiles	1.0	null
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
GSE202434,GSE202438_6_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Prenatal Exposure Delayed Effects	CTD Gene-Disease Associations	1.0	1.80961
Lung carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.858
PMC4856960-supp_gkv1471_nar-01762-z-2015-File012.xlsx-GO_common_7H-HIF1_chip-Common_elements_in_chip7h_and_chip_hif1_2530_official_gene_symbols_HIF1A	Rummagene Transcription Factor Associations 2026	1.0	null
primary visual cortex (striate cortex, area V1/17)_30 yrs_F_12290	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.888586
GSE229973_3_v_7_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
REST_SK-N-SH_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Congenital Contractural Arachnodactyly	DisGeNET Gene-Disease Associations	1.0	null
GSE220806_1_v_3_progesterone_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_2363_KD_ZNF589_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	13.8557
inner SZ in lateral temporal-occipital cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.931845
PMC6683136-41598_2019_47363_MOESM2_ESM.xlsx-GENE_SET-Positive_correlation_of_ZEB1-AS1_and_other_genes_ZEB1	Rummagene Transcription Factor Associations 2026	1.0	null
GTEX-WHSE-0011-R11A-SM-3P5YY	GTEx Tissue Sample Gene Expression Profiles	1.0	0.863775
Perturb_14988_KO_Phf8_SRP093797	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-5.18298
496100562_FWM_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.69759
Perturb_15457_KO_GPRC5A_SRP165862	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.15783
MAFK_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8279_KD_ZNF622_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GSE203181_0_v_1_phosphoramidon_human	RummaGEO Drug Perturbation Signatures	1.0	null
FOXA2_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14286_OE_YAPS94A_SRP336792	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K4me2_A549_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
ubiquitin-like protein ligase activity	GO Molecular Function Annotations 2025	1.0	null
ELF1_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-37-4135-01A-01R-1100-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE111660_1_v_3_prdm16_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_572_KO_Plod1_SRP321648	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	11.9546
POLR2AphosphoS5_GM12892_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HCFC1	ENCODE Transcription Factor Targets	1.0	null
KYSE220	DepMap CRISPR Gene Dependency	1.0	2.75123
rostral periolivary nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.56107
E2F4_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE223893_1_v_10_setd2_human	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_8280_KD_DDX5_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.80902
H3K4me1_megakaryocyte_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
G22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.863172
H3K4me3_Stomach Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
HOXC9	ChEA Transcription Factor Targets	1.0	null
YY1_ECC-1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8084_KD_CELF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
primary motor cortex (area M1, area 4)_3 yrs_F_12836	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.955985
NCI-H847	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.27705
POU2F2_GM12878_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GATA1_G1E-ER4_mm9_7	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PPARG	JASPAR Predicted Transcription Factor Targets	1.0	null
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.47966
WBP4	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.04529
Perturb_12372_KD_SKP2_SRP297799	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.89363
Rimonabant_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0341633
H3K4me3_cerebellum_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_4904_KO_NSUN6_SRP233222	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
NCIH1435	CCLE Cell Line Gene CNV Profiles	-1.0	-1.79766
SETDB1	ENCODE Transcription Factor Targets	1.0	null
Tumor Progression	DisGeNET Gene-Phenotype Associations	1.0	null
GTEX-T5JC-0011-R9A-SM-32PLV	GTEx Tissue Sample Gene Expression Profiles	1.0	1.25498
Perturb_6759_KO|KD_IER5_SRP103746	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.3835
TAL1_MEL cell line_mm9_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8154_KD_CPSF6_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.34713
Perturb_1206_KO_Sp3_SRP302435	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-3.02519
Perturb_11716_KD_GATAD2A_SRP194625	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.40954
Cortical amygdalar area, posterior part, medial zone, layer 2	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.60938
HCC38	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.03828
Perturb_3656_KO_MTHFD1_SRP120974	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
GTEX-UTHO-0011-R2A-SM-3GIKC	GTEx Tissue Sample Gene Expression Profiles	1.0	1.2455
PAX6-23342162-BETA-FORBRAIN-LENS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
ALX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.3455
superficial part of arcuate nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.72548
NRF1_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14328_KD_GRHL2_SRP157074	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.87234
Pheochromocytoma and Paraganglioma_PCPG_TCGA-RW-A681-01A-11R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
ATF2_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_Rectal Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
abnormal embryonic neuroepithelium morphology	MGI Mouse Phenotype Associations 2023	1.0	null
hsa-miR-3646	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.921135
Medial geniculate complex, medial part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.12025
Perturb_15436_KD_NUSAP1_SRP074246	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.855
FOXD2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	62.451
Perturb_3947_KD_RNF6_SRP126561	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.45499
Ezh2_Deficiency_GDS4309_364_mouse_Hearts	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GSE246195,GSE246305_1_v_0_sin3a_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CDX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.0013
CHSA8926	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Liver carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.637
IRF1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE202434,GSE202438_8_v_5_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
regulation of signaling	GO Biological Process Annotations 2015	1.0	null
GSE120612_7_v_1_etoposide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
LoVo cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.037
Sarcoma_SARC_TCGA-DX-A2IZ-01A-11R-A21T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
rnf2_20805357_u2os_osteosarcoma_lof_human_gpl570_gse23035	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.400776
GSE195568_2_v_0_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_11922_KD_CD73_SRP197630	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.13697
PMC5263239-mmc2.xls-SEM_siMLL-AF4-MLL-AF4_gene_targets_significantly_downregulated_739_unique_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
CEBPB_IMR-90_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE224294_3_v_2_ngly1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
hsa-miR-335	TargetScan Predicted Conserved microRNA Targets	1.0	0.09606
Female reproductive system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.672
PMC11046918-12967_2024_5211_MOESM5_ESM.xlsx-C_FUS-DDIT3-eGFP_vs_eGFP-Table_S3_Regulated_genes_between_scaffold-cultured_HT1080_FUS_DDIT3-eGFP_cells_and_control_cell_lines_DDIT3	Rummagene Transcription Factor Associations 2026	1.0	null
GSE146982_4_v_1_gpd1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Memory Disorders	CTD Gene-Disease Associations	1.0	1.06152
Perturb_17650_KD_AFF4_SRP334520	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.69611
Retinoblastoma cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.007
bed nucleus of the stria terminalis, mediocentral division	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.28671
Perturb_16480_KO_Ring1a/Ring1b_SRP136563	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-4.60387
MAX_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Glioblastoma	DisGeNET Gene-Disease Associations	1.0	null
intracellular part	LOCATE Predicted Protein Localization Annotations	1.0	null
H3K4me1_bone marrow_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
ESR2	Pathway Commons Protein-Protein Interactions	1.0	null
Perturb_16953_KO_MLX_SRP183152	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.22841
H3K4me3_cardiac mesoderm_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_skeletal muscle myoblast_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15634_KO_AHCY_SRP351305	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.20081
MSX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.6628
OAW28	CCLE Cell Line Gene CNV Profiles	1.0	1.45273
H3K4me3_myocyte_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K27me3_T-cell acute lymphoblastic leukemia_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE110708_1_v_3_adar_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
TM31	CCLE Cell Line Gene CNV Profiles	-1.0	-3.21049
GSE146074_0_v_11_ly6e_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Olfactory areas	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.25268
fulvestrant_homo sapiens_gpl570_gse22533	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
HCC1569	COSMIC Cell Line Gene Mutation Profiles	1.0	null
GSE130690,GSE130692_2_v_0_sirt6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Crus I, right, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.00869
GSE183041_1_v_0_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
Thymol_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0211503
Perturb_2520_KD_JUN_SRP357624	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.64552
striatum_12 pcw_F_12960	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.898449
H3255	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
H3K4me3_HEK293_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_15393_KD_CHKA_SRP050331	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
PCBP3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-3.00989
Gastric cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.174
spinal trigeminal nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.849548
Perturb_6044_KD_NCOA7_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GTEX-QMR6-0011-R4A-SM-32PKU	GTEx Tissue Sample Gene Expression Profiles	1.0	1.25695
H3K18ac_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
hsa-miR-370	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
GSE128730_4_v_6_neratinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_7911_KO_LIN52_SRP367036	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.0311
cell part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
ABC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.44247
APAF1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.04539
hsa-miR-509-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
GTEX-WZTO-0011-R5B-SM-3NMC5	GTEx Tissue Sample Gene Expression Profiles	1.0	1.91001
FOXP1-21924763-HESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Reticular nucleus of the thalamus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.15575
Perturb_6217_KO_Mef2d_SRP227204	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	8.90933
Head and Neck squamous cell carcinoma_HNSC_TCGA-DQ-7591-01A-11R-2081-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_7853_KD_CCNF_SRP212181	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	14.2811
ESR1	Hub Proteins Protein-Protein Interactions	1.0	null
Head and Neck squamous cell carcinoma_HNSC_TCGA-CR-7371-01A-11R-2016-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE125153_2_v_0_bcl3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-E1-A7YM-01A-11R-A34F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_8269_KD_METAP2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.64553
Cortical amygdalar area, anterior part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.13832
HCC-4006 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.543
GSE109530,GSE109531_2_v_0_hdac3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
RUNX3	ENCODE Transcription Factor Targets	1.0	null
Renal carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.262
Perturb_12738_KD_TCF7L1_SRP094619	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.60252
C32TG	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.02533
Perturb_12350_KD_CDC73_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.0173
JJ012	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.47494
H3K4me3_limb_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
paracentral lobule, posterior part, right, lateral bank of gyrus	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.14687
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.7463
Perturb_477_OE_ACE2_SRP278541	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.54383
Reproductive organ cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.811
olfactory part of entorhinal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.18399
Perturb_7179_KO_TrEx_SRP163035	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.23833
SNU81	DepMap CRISPR Gene Dependency	1.0	3.42631
KDM5A_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8278_KD_UTP3_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.2296
heart muscle	HPA Tissue Gene Expression Profiles	-1.0	-0.846323
layer 2 of FCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.47502
SP1_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Prostate adenocarcinoma_PRAD_TCGA-EJ-5497-01A-02R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE240439_1_v_2_decitabine_human	RummaGEO Drug Perturbation Signatures	1.0	null
Liver	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
H3K4me1_fibroblast of lung_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8283_KD_BCLAF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.8053
Perturb_16496_KO_Ptpn2_SRP159185	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-2.17189
NSG1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.10703
Perturb_6512_KD_ALKBH5_SRP090686	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.6959
PMC4821877-ncomms10846-s9.xlsx-THP1_Splice_events-Gene_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
PMC8452624-41467_2021_25709_MOESM12_ESM.xlsx-ST12-Unnamed_2_KLF6	Rummagene Transcription Factor Associations 2026	1.0	null
H3K9ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE102505_4_v_3_tunicamycin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE228106_3_v_1_paclitaxel_human	RummaGEO Drug Perturbation Signatures	-1.0	null
biological regulation	GO Biological Process Annotations 2015	1.0	null
Hypertrophy	CTD Gene-Disease Associations	1.0	1.32876
STAT5A_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-4762-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.7397
KAT2B	ENCODE Transcription Factor Targets	1.0	null
GTEX-R55E-2526-SM-2TC6H	GTEx Tissue Sample Gene Expression Profiles	1.0	1.04977
GSE157960_2_v_1_progesterone_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	42.8011
KYSE-180	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1236
V, left, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.14775
GSE109285_5_v_2_glucagon_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE172295_3_v_2_sh3gl1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
FOXC2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	64.6624
GSE199204,GSE211619_4_v_0_glutamine_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE164874_5_v_3_prednisolone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
ventral juxtacommissural pretectal nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.26416
AKAP5	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.45971
posterior (caudal) superior temporal cortex (area 22c)_3 yrs_F_12836	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.913382
Perturb_10003_KD_GPKOW_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.62301
Piriform-amygdalar area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.14599
H3K4me3_ES-E14_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
Frontal pole, cerebral cortex	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.02974
KDM4A_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Kidney renal papillary cell carcinoma_KIRP_TCGA-BQ-5890-01A-11R-1592-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE70499_5_v_2_bmal1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_14126_KO_TP53/CDKN2A/PTEN_SRP258861	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.45637
ZNF418	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	50.762
Perturb_6096_KD_ZNF326_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_13755_KD_KLF3/KLF4_SRP233218	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.07284
carcinogenesis	GeneRIF Biological Term Annotations	1.0	null
POLR2A_H54_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE154936_3_v_2_remdesivir_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-XMD1-0011-R11A-SM-4AT5J	GTEx Tissue Sample Gene Expression Profiles	1.0	1.58463
CTCF_B cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-WHSE-0011-R7A-SM-3P5YZ	GTEx Tissue Sample Gene Expression Profiles	1.0	0.998359
Perturb_8239_KD_RECQL_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.96097
NANOG	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.36085
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-2.38844
WDR5	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.07382
Perturb_11541_Mut_KRAS_SRP175175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.61736
Lung adenocarcinoma_LUAD_TCGA-55-7994-01A-11R-2187-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
layer 1 of AOD cortex	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.22144
Main olfactory bulb, outer plexiform layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.04539
Perturb_14588_KD_TCF7L1_SRP094619	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.21481
KDM4A	ENCODE Transcription Factor Targets	1.0	null
mantle zone of AOD	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07423
TAF1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
cingulum bundle, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	2.08878
H2AFZ_B cell_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_17538_KO_MAPK7_SRP265870	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.76211
GSE160001,GSE160670_3_v_2_lapatinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
empty decidua capsularis	MGI Mouse Phenotype Associations 2023	1.0	null
GSE181513_0_v_1_usp7_human	RummaGEO Gene Perturbation Signatures	-1.0	null
E2F1-26619117-HEPATOCYTES-MOUSE-LIVER	ChEA Transcription Factor Targets 2022	1.0	null
GSE88819_0_v_8_tug1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE151090_2_v_1_verteporfin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
hsa-miR-21-5p	MiRTarBase microRNA Targets	1.0	null
Kidney renal papillary cell carcinoma_KIRP_TCGA-P4-A5EA-01A-11R-A28H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_16533_KO_Cdk8_SRP351257	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	9.17221
CTCF_02_185	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.62847
EN1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.1633
ZBTB7A_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_12253_KO|KD_SDHB|SDHA_SRP128515	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.18619
Perturb_16361_KD_VDR_SRP057721	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Pancreatic adenocarcinoma_PAAD_TCGA-YH-A8SY-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
NUGC-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.95007
GSE102467_1_v_0_pazopanib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE211128_4_v_0_angptl4_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE189609_1_v_0_hax1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
TBL1XR1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
III	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.993952
CTBP2_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ESET-19884257-ESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
ZNF217_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Eplerenone_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0137481
Brain Lower Grade Glioma_LGG_TCGA-HT-7620-01A-11R-2256-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HUG1N	CCLE Cell Line Gene CNV Profiles	1.0	1.38449
Prostate adenocarcinoma_PRAD_TCGA-CH-5750-01A-11R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Intestinal disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.688
GTEX-R55E-0011-R7A-SM-2TC5Z	GTEx Tissue Sample Gene Expression Profiles	1.0	1.74179
Perturb_4257_KD_AR_SRP184695	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.56468
ISX	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.7653
nucleus subceruleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.927198
accumbens nucleus, core domain	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.29105
H3K4me3_MEL cell line_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_BJ_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE179868,GSE180330_1_v_0_ddx21_human	RummaGEO Gene Perturbation Signatures	-1.0	null
ribavirin_homo sapiens_gpl570_gds4391	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
POLR2A_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27me3_cardiac mesoderm_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_A549_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
NCI-H1930	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.47573
GSE122101,GSE122103_0_v_4_ssu72_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
TTC30A	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.4232
H3K4me3_GM12878_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
CAL62	CCLE Cell Line Gene Expression Profiles	1.0	1.97462
Perturb_11409_KD_ESRP1/ESRP2_SRP191570	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.04338
H3K27ac_A549_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_SK-N-SH_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8083_KD_FASTKD2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.82641
GSE200352_5_v_8_pparg_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_7949_Mut_BAZ1A_SRP100570	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.30352
COR-L47	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.36569
Perturb_2114_KD_SF3B3_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.80813
GSE114992,GSE114993_1_v_2_irf5_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CTCF_GM19238_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
metal ion binding	GO Molecular Function Annotations 2015	1.0	null
Perturb_8128_KD_CIRBP_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.39239
GSE223008_5_v_12_calhm6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
ERF::HOXB13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.7991
Perturb_440_KD_PRMT5_SRP073189	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.42686
CTCF_MCF-7_hg19_9	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_7266_OE_OspC1_SRP368098	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.88534
LP-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.869532
ubiquitin-like protein ligase activity	GO Molecular Function Annotations 2023	1.0	null
PMC7405480__F2	PFOCR Pathway Figure Associations 2023	1.0	null
Perturb_12361_KD_SF3B5_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.05028
Perturb_10253_KO_WT1_ERP126063	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.31851
Perturb_12268_KO_CECR1_SRP255026	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	5.73654
GSE160817_4_v_9_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
8680_TANGO6_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.53088
Lung adenocarcinoma_LUAD_TCGA-55-6968-01A-11R-1949-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2575_KD_LINE1_ERP011233	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	12.7455
Perturb_12235_KD_CHD4_SRP190500	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
ZNF211	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.4899
PMC12048643-44318_2025_409_MOESM3_ESM.xlsx-regulonTargets-PBX3_PBX3	Rummagene Transcription Factor Associations 2026	1.0	null
HCFC1_ES-E14_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
non-small cell lung cancer cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.51
fastigial nucleus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.900659
GB1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.41884
Mdr2_KO_GDS1990_286_mouse_Livers of 12 month old	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
neurod1_17630985_pineal_gland_lof_mouse_gpl1261_gds3000	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.863414
GTEX-T5JC-0011-R2A-SM-32PLZ	GTEx Tissue Sample Gene Expression Profiles	1.0	2.01333
Perturb_8055_KD_IGF2BP3_SRP094100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.6349
DMRT1-23473982-TESTES-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
EBF1	ENCODE Transcription Factor Targets	1.0	null
GSE202434,GSE202438_9_v_11_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_6879_KD_LINC00857_SRP371132	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.98035
GTEX-X585-0011-R4B-SM-46MVH	GTEx Tissue Sample Gene Expression Profiles	1.0	1.34966
absent amniotic cavity	MGI Mouse Phenotype Associations 2023	1.0	null
GTEX-WZTO-0011-R1B-SM-3NMAR	GTEx Tissue Sample Gene Expression Profiles	1.0	2.264
GSE166783_1_v_2_tp53_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_3850_KD_AKAP12_SRP254561	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.08623
Lewis lung carcinoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.769
Perturb_17531_KO_CD44_SRP256345	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.62176
LGE-VZ border region	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.22295
FOXM1_ECC-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PCDH18	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.2843
Sarcoma_SARC_TCGA-DX-A8BU-01A-11R-A37L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE226249_0_v_8_pirfenidone_human	RummaGEO Drug Perturbation Signatures	1.0	null
496100620_FWM_possible Alzheimer's disease_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.08613
SW 1990	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.858999
GTEX-T5JC-0011-R4A-SM-32PLT	GTEx Tissue Sample Gene Expression Profiles	1.0	1.01976
GSE111247_14_v_3_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
ZBED1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.1337
TCFCP2L1-18555785-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
Perturb_10075_KD_AQR_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.261
Prostate adenocarcinoma_PRAD_TCGA-EJ-5514-01A-01R-1580-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTAGE6	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.70275
KYM-1	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Perturb_8273_KD_RPS19_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H2AB1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.01741
H3K4me3_fibroblast of the aortic adventitia_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_8205_KD_PCBP2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.74773
PMC9314667-Table_1.xlsx-Regulons-SOX9_SOX9	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me3_GM12875_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_5447_KD_MED1_SRP395995	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.0803
TAF1_GM12891_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NB4	Sanger Dependency Map Cancer Cell Line Proteomics	1.0	2.14083
GSE210770_0_v_1_foxp1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Respiratory failure	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.023
Azithromycin (hydrate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0192407
GSE153836_14_v_5_fluoxetine_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
SNU899	CCLE Cell Line Gene CNV Profiles	1.0	1.48621
Perturb_12933_KD_CDK9_SRP340404	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.0844
HOXB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.1324
hsa-miR-19b-3p	MiRTarBase microRNA Targets	1.0	null
JOPACA1	DepMap CRISPR Gene Dependency	1.0	4.50181
GSE130956_0_v_3_icaritin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
G130	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.921555
SNU387	DepMap CRISPR Gene Dependency	1.0	2.27845
intracellular	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
GSE210682_2_v_3_methadone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC11947124-41419_2025_7562_MOESM1_ESM.docx-63-ENSG00000198816_ZNF358	Rummagene Transcription Factor Associations 2026	1.0	null
PMC6715699-41467_2019_11785_MOESM4_ESM.xlsx-CSL_KD-Unnamed_1_AR	Rummagene Transcription Factor Associations 2026	1.0	null
POLR2A_GM18951_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
intracellular organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
CTCF_GM12873_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_282_KD_IMPDH1_SRP251285	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_9061_KD_NANOG_SRP100928	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
HOXC9-25013753-NEUROBLASTOMA-BE2-C-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_2328_KD_SF3B5_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.12523
H3K4me3_choroid plexus epithelial cell_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_15574_KD_NUSAP1_SRP074246	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Neurodegenerative disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.3
Perturb_2797_KD_RORC_SRP066204	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Medial amygdalar nucleus, anteroventral part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.14445
H3K4me1_bone marrow macrophage_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-51-6867-01A-11R-2045-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
2019_DACH2_ENST00000373125.4,ENST00000373131.1	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.579173
Perturb_14892_KO_H11_ERP118037	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.5393
GTEX-X4XX-0011-R6B-SM-46MWP	GTEx Tissue Sample Gene Expression Profiles	1.0	0.931774
PMC4686761-ncomms10068-s3.xlsx-S2G-MSC_down_specific-Supplementary_Data_2G_-_expression_of_down-regulated_genes_2_fold_change_specifically_in_MSC_PTEN-_-_vs_MSC_PTEN_MSC	Rummagene Transcription Factor Associations 2026	1.0	null
NFYA_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H2BK12ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
hsa-miR-1273e	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.40969
hsa-miR-214	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.40969
Cardiovascular system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.299
facial nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.957972
GSE86507,GSE86509_7_v_2_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
DMRT1	ChEA Transcription Factor Targets	1.0	null
Perturb_1345_KD_ARID1A_SRP336358	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K4me1_olfactory bulb_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE195582_3_v_1_pim1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_757_KO_DNMT3B_SRP389363	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.02306
PMC12824906-mmc5.xlsx-Sheet1-Table_S4_Target_genes_of_FOXM1_and_their_expression_across_the_subtype_of_breast_tumors_FOXM1	Rummagene Transcription Factor Associations 2026	1.0	null
GTEX-S7SE-0011-R6A-SM-2XCD9	GTEx Tissue Sample Gene Expression Profiles	1.0	1.02334
ATF2_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2528_KO_TET2_SRP163132	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.06821
SRD5A1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.29651
lymphnode_5a	HPA Tissue Sample Gene Expression Profiles	1.0	1.5643
RUNX1_01_22	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.62182
SK-MEL-30	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.833626
H3K4me3_HL-60_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K27ac_keratinocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE217694_3_v_2_pold1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Penis Foreskin Keratinocyte Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_15506_KD_MED1_SRP179971	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Osteosarcoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.242
Eosinophil percentage of white cells	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.969897
PMC10709142-41556_2023_1281_MOESM2_ESM.xlsx-Supplementary_Table_1-CLUSTER_2_MAF_downregulated_MAF	Rummagene Transcription Factor Associations 2026	1.0	null
POLR2AphosphoS5_Panc1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-PW2O-1726-SM-2S1OO	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09796
morphine_mus musculus_gpl6246_gse17731	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
Retrosplenial area, lateral agranular part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.3805
hippocampus (hippocampal formation)_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.26963
H3K4me3_megakaryocyte_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
midline nuclear complex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.26744
FLI1	ChEA Transcription Factor Targets	1.0	null
CHD4_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MAX_H1-hESC_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_GM12871_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
caudate nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.52591
CPC-N	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.906075
ubiquitin protein ligase activity	GO Molecular Function Annotations 2025	1.0	null
KLF4-19030024-MESC-mouse	ChEA Transcription Factor Binding Site Profiles	1.0	null
HA-E2F1_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-T6MN-0011-R11A-SM-32QOX	GTEx Tissue Sample Gene Expression Profiles	1.0	0.848521
Doxycycline (monohydrate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0219261
G112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.16283
Perturb_17210_KD_JUN_SRP188712	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.2708
III, right, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-0.986945
Breast cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.793
ECV-304 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.55
eGFP-JUNB_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE88819_0_v_2_tug1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
CHD1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Anxiety Disorders	CTD Gene-Disease Associations	1.0	1.54451
Coronavirus infectious disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.307
Lung squamous cell carcinoma_LUSC_TCGA-63-A5MB-01A-11R-A26W-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
PMC6225799-annrheumdis-2018-213524supp003.xlsx-Activated-state-LPS-Gene_Symbol_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me3_A549_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_10698_KD_CD274_SRP307356	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.37092
GTF2F1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-UTHO-0011-R3A-SM-3GIK8	GTEx Tissue Sample Gene Expression Profiles	1.0	0.890922
POU2F2_GM12891_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-GV-A3QI-01A-11R-A220-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Nodulus (X)	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.07007
PMC11352684__F4	PFOCR Pathway Figure Associations 2024	1.0	null
Aspartate aminotransferase levels	GWAS Catalog SNP-Phenotype Associations 2025	1.0	0.869897
GSE167474_1_v_3_naa40_human	RummaGEO Gene Perturbation Signatures	-1.0	null
AGS	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Perturb_489_KD_DDX17_SRP360079	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.02177
SAP30_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H2135	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.867132
TAF1_GM12892_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC10789969-crt-2023-577-Supplementary-Table-S2.pdf-17-TFDP2_TFDP2	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_12314_KO_AGO1_SRP136692	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
H3K27ac_Panc1_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
FOXP2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-3.30014
Perturb_12570_KD_MSI1_SRP185353	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.19965
GSE196699_2_v_1_prdm16_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
VI, right, paravermis	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.52808
MYC_K562_hg19_6	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC8684775-CTM2-11-e640-s002.xlsx-Sheet1-Table_S3_MAF_file_of_the_CCS_samples_MAF	Rummagene Transcription Factor Associations 2026	1.0	null
RPMI 8226	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.98201
Perturb_7429_KO|KD_RBFOX2|HNRNPM_SRP068106	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.81163
NFE2	ENCODE Transcription Factor Targets	1.0	null
Perturb_7737_KD_HRSP12_SRP155278	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.3865
FOXA2_A549_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-QMR6-0011-R8A-SM-32PKJ	GTEx Tissue Sample Gene Expression Profiles	1.0	0.860093
GSE202434,GSE202438_9_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
mantle zone of JcPV	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.09167
paraventricular nucleus of hypothalamus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.13762
GSE111660_4_v_3_prdm16_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_14184_KO_KDM1A_SRP289469	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.20215
emboliform nucleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.08315
Perturb_6141_OE_PPP1CA/PPP1R8_SRP118980	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.45058
Head and Neck squamous cell carcinoma_HNSC_TCGA-BA-6871-01A-11R-1873-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
polysensory temporal cortex (area 22p)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.941541
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.00349
GSE223008_5_v_2_calhm6_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me1_small intestine_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
HO-8910PM	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.934
Perturb_5623_KD_SOX2_SRP307776	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.54878
GTEX-NPJ7-0011-R9a-SM-2TC5R	GTEx Tissue Sample Gene Expression Profiles	1.0	1.4322
sirolimus_rattus norvegicus_gpl6247_gse35048	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
TCFCP2L1-18555785-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
PMC4856960-supp_gkv1471_nar-01762-z-2015-File010.xls-Genes_5kb_E2F7_Hyp-gene_name_E2F7	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_1094_KO_ATXN1L_SRP230198	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.34759
CTCF_astrocyte of the spinal cord_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
YY1	MotifMap Predicted Transcription Factor Targets	1.0	null
10023_ZC3H18_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.506593
GSE218378_1_v_0_pbx1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-EK-A2GZ-01A-11R-A180-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
CTCF_fibroblast of the aortic adventitia_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Serum Total Cholesterol Measurement	DisGeNET Gene-Phenotype Associations	1.0	null
GTEX-N7MS-0011-R7a-SM-2HMKN	GTEx Tissue Sample Gene Expression Profiles	1.0	1.37249
Edema	CTD Gene-Disease Associations	1.0	1.06225
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.932553
GTEX-XOTO-0011-R8A-SM-4B65J	GTEx Tissue Sample Gene Expression Profiles	1.0	0.854316
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-9_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_7490_KD_SIN3B_SRP173465	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.5578
H3K4me3_H1 Derived Mesenchymal Stem Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE209898,GSE209899_0_v_1_flcn_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Bile duct adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.435
hsa-miR-16	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.965816
Perturb_6434_KD_HOXA10AS_ERP131886	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.19965
Perturb_80_KD_CENPA1_SRP187530	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
NCIH650	DepMap CRISPR Gene Dependency	1.0	2.0668
Perturb_443_KD_SBF2AS1_SRP116042	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.069
Perturb_8920_KD_P300_SRP256204	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.36585
Head and Neck squamous cell carcinoma_HNSC_TCGA-CQ-A4CI-01A-11R-A266-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_12945_KD_METTL3_SRP106608	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.5758
SUZ12_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE115542_5_v_3_digoxin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE218580_1_v_4_fentanyl_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
UBTF	ENCODE Transcription Factor Targets	1.0	null
MYC	ChEA Transcription Factor Targets	1.0	null
Perturb_409_KO_IRE1_SRP353826	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.27116
Secondary motor area, layer 5	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.38138
negative regulation of intracellular signal transduction	GO Biological Process Annotations 2025	1.0	null
GSE133213_11_v_3_znrf3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
COV504	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.31817
H3K9ac_CD14-positive monocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
CTCF_keratinocyte_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_5562_KO_MTSS1_SRP266832	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.86444
VIIIB	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.10395
Head and Neck squamous cell carcinoma_HNSC_TCGA-CR-7385-01A-11R-2016-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE195568_2_v_10_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Central Neuroblastoma	DisGeNET Gene-Disease Associations	1.0	null
ZKSCAN1_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE143994_2_v_1_ythdf1_human	RummaGEO Gene Perturbation Signatures	1.0	null
DAOY cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.553
centromedian nucleus of thalamus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.849606
6555_POLR3A_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.507588
Colorectal cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.743
periventricular nucleus, preoptic portion	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-2.41263
H3K9ac_ES-Bruce4_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
STAT3_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Ovary	BioGPS Human Cell Type and Tissue Gene Expression Profiles	1.0	1.32675
Mitoxantrone (dihydrochloride)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0353484
GSE229309,GSE229314_4_v_1_elavl1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
EMX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.3951
GSE129244_0_v_5_lmo2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Cholangiocarcinoma	DisGeNET Gene-Disease Associations	1.0	null
Cervix Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
MYOG	ENCODE Transcription Factor Targets	1.0	null
Perturb_11692_KD|OE_SF3A3|MYC_SRP253943	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.02936
MYCN	ChEA Transcription Factor Targets	1.0	null
Perturb_6262_KD_NDP_SRP188348	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
MAFK_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE116810_2_v_0_selinexor_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_16432_OE_E2f4_SRP327850	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	15.7825
DLX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	13.8658
GSE71674,GSE71676_0_v_2_cbfa2t2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
hippocampus (hippocampal formation)_12 pcw_F_12835	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	0.945783
DT-061_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	1.0	0.0220246
Main olfactory bulb	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.05427
GSE58724_3_v_4_oxymetholone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
CHD2_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8347_KD_YY1_SRP286033	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.12454
GSE111247_11_v_5_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
NCI-H2030	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.865561
Perturb_14085_KD_GAS41_SRP110132	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me1_Fetal Brain	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
SMAD6	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.58926
Secondary Malignant Neoplasm Of Liver	DisGeNET Gene-Disease Associations	1.0	null
Bed nuclei of the stria terminalis, anterior division, rhomboid nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.51424
negative regulation of I-kappaB kinase/NF-kappaB signaling	GO Biological Process Annotations 2023	1.0	null
Rectum adenocarcinoma_READ_TCGA-DC-6156-01A-11R-1660-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
TEAD4_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE239844_11_v_10_crizotinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE82032_3_v_1_trametinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_3193_KO_DLAT_SRP266195	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Perturb_2872_Mut_KRAS_SRP404927	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.31682
HS 294T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.900368
GSE164874_5_v_10_prednisolone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE102486,GSE102490_1_v_5_setdb1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
IPC-298	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.1622
superior colliculus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.86963
GSE185944_0_v_3_pth1r_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_12801_KD_Spi1_SRP295556	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	8.63976
Perturb_8163_KD_SRSF3_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.552
MXI1_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Secondary motor area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.44807
CEBPZ_02_118	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.60716
GSE195568_3_v_0_palbociclib_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE110268_2_v_3_foxd1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE57871_1_v_2_vorinostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Tauopathy	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.034
FLI1-21571218-MEGAKARYOCYTES-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
intrinsic component of membrane	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
GTEX-XMD1-2826-SM-4AT5F	GTEx Tissue Sample Gene Expression Profiles	1.0	1.25878
intermediate stratum of r10Tr	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.05732
Perturb_15635_KO_MAT2A_SRP351305	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.30831
POU3F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.6482
Prostate adenocarcinoma_PRAD_TCGA-HC-A4ZV-01A-11R-A26U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
alitretinoin_homo sapiens_gpl6480_gse43090	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
NCI-H2170	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32505
TCF12_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PPARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	49.5601
PMC4067464-onc2013378x3.xls-Sheet1-Supplementary_Table_1_Top_1000_E2F4_Chip-Seq_targets_that_are_repressed_by_p53_E2F4	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_12365_KD_WBP11_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.42097
regulation of response to stimulus	GO Biological Process Annotations 2015	1.0	null
GSE192663_1_v_5_acly_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC5263239-mmc2.xls-SEM_-_MLL-AF4-Non-spreading_targets_gene_names_2497_unique_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me3_fibroblast of upper leg skin_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE89057_0_v_1_sox5_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Infralimbic area, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.01659
HdhQ111/111_Knock-in_GDS4534_744_mouse_Striatum and cerebellum	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
Perturb_12313_OE_APT1_SRP120630	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.73847
Perturb_14021_OE_MIR722_SRP185837	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE86507,GSE86509_4_v_1_hoxb7_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_9939_KD_KIF1C_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.21755
layer 6 of PrS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.34853
Perturb_11384_KD_CIT_SRP173646	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.73345
GSE215086_1_v_7_batf_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Prostate carcinoma	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
Perturb_6056_KD_QKI_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE192663_1_v_2_acly_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
H3K4me3_HepG2_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
OVCAR8	DepMap CRISPR Gene Dependency	1.0	2.08549
H3K4me3_SK-N-SH_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_GM12865_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
septopallidal transition area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.34181
H2AFZ_myotube_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
JUND_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
globose nucleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.34742
H3K4me1_skeletal muscle myoblast_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
skeletalmuscle_a	HPA Tissue Sample Gene Expression Profiles	-1.0	-1.35411
Perturb_17212_KD_GRHL2C_SRP124640	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.4773
MYBL1_KO_GDS4485_350_mouse_Testis from 17 day old	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
GSE248045,GSE248046_0_v_2_runx1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
medial part of r2B	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.91812
layer 4 of PaS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.3627
Perturb_12851_KO_Tet2_SRP338315	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	7.95208
Perturb_8449_KD_LETN_SRP230777	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.61029
Lung non-small cell carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.859
H3K4me3_kidney epithelial cell_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_Colonic Mucosa	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_12355_KD_PRPF31_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.97245
Perturb_8294_KD_TFIP11_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.8185
globus pallidus, internal segment, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.35634
GSE160304,GSE163392_7_v_3_zswim8_human	RummaGEO Gene Perturbation Signatures	1.0	null
CTCF_GM12865_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
E2F6_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HT-115	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles	1.0	null
H3K4me1_GM12878_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_7913_KO_ZNF335_SRP367036	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.46102
GSE179868,GSE180330_1_v_2_ddx21_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_10004_KD_KRR1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.18536
GSE181003_3_v_0_selinexor_human	RummaGEO Drug Perturbation Signatures	-1.0	null
layer 3 of PrS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.41918
CTCF_HeLa-S3_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-QVJO-0011-R6A-SM-2S1QN	GTEx Tissue Sample Gene Expression Profiles	1.0	1.27871
GTEX-N7MT-0011-R7a-SM-2I3FZ	GTEx Tissue Sample Gene Expression Profiles	1.0	1.19974
HSC4	DepMap CRISPR Gene Dependency	1.0	9.04787
GSE203308_14_v_5_brf1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
Malignant astrocytoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.442
Epithelial Ovarian Cancer	DisGeNET Gene-Disease Associations	1.0	null
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60142
ELF1_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GATA3_T47D_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC7773022__F9	PFOCR Pathway Figure Associations 2024	1.0	null
PMC6459557-pbio.3000201.s012.xlsx-Sheet1-FOXD1_FOXD1	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_14609_KD_SIK3_SRP118895	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.16712
CTCF_fibroblast of skin of abdomen_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H1882	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.00206
Lung squamous cell carcinoma_LUSC_TCGA-46-3768-01A-01R-0980-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE142210_2_v_0_panobinostat_human	RummaGEO Drug Perturbation Signatures	1.0	null
PEO4	DepMap CRISPR Gene Dependency	1.0	2.05526
GSE219274,GSE219276_2_v_1_doxorubicin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE146074_10_v_8_ly6e_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
SPI1	ENCODE Transcription Factor Targets	1.0	null
parietal neocortex_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.4118
ABCA1_OE_GDS2303_189_mouse_LDL receptor-deficient livers	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
CTCF_fibroblast of mammary gland_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE197850_4_v_2_glucagon_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GTEX-R55E-0011-R1A-SM-2TC6N	GTEx Tissue Sample Gene Expression Profiles	1.0	0.896939
Skin Cutaneous Melanoma_SKCM_TCGA-EE-A2M5-06A-12R-A18S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE203308_4_v_3_brf1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
ZNF263_HEK293_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-X4XX-0011-R1B-SM-3P622	GTEx Tissue Sample Gene Expression Profiles	1.0	1.23206
mediodorsal nucleus of thalamus_8 yrs_M_12841	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.983103
POLR2A_cortical plate_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
COR-L47	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.885611
GSE100316_0_v_2_mtor_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GTEX-QMR6-1426-SM-32PLA	GTEx Tissue Sample Gene Expression Profiles	1.0	1.23962
GSE144443_5_v_1_nicotinamide_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Orbital area	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.20504
Superior colliculus, motor related, deep white layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.17406
Perturb_8293_KD_SUPV3L1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_5735_KD_NAP1L3_SRP121475	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.87275
STAT5A_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_8191_KD_ILF2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.9866
Perturb_11525_KD_SNW1_SRP092641	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.52717
internal globus pallidus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.37848
H3K4me3_fibroblast of pulmonary artery_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE151494_1_v_9_nrp1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
PMC8052288-mmc4.xlsx-PAF_DREAM_targets_H1792-Unnamed_1_KCNIP3	Rummagene Transcription Factor Associations 2026	1.0	null
EZH1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.56946
BHLHE40_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
VIIB	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.09348
Perturb_4237_OE_ERG/FLI1_SRP403488	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.43794
H3K4me3_fibroblast of lung_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
GSE180982_1_v_0_mlst8_human	RummaGEO Gene Perturbation Signatures	1.0	null
Bladder Urothelial Carcinoma_BLCA_TCGA-DK-A3IQ-01A-31R-A32Y-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
TEAD4_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE92457_9_v_12_ethanol_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Brain cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.079
MAZ_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_9924_KD_RBM22_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.43139
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-6_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-TM-A7CF-02A-11R-A32Q-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_2778_KD_ZNF589_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Clear cell renal cell carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.047
Medulloblastoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.784
Perturb_18443_KD_YAP1/WWTR1/CGAS_SRP303519	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.39131
Perturb_2721_KD_YAP1/WWTR1_SRP115100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
PMC6715699-41467_2019_11785_MOESM4_ESM.xlsx-CSL_KD-Genes_differentially_expressed_upon_CSL_silencing_AR	Rummagene Transcription Factor Associations 2026	1.0	null
CTCF_H54_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_Colon Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-EE-A2GK-06A-11R-A18S-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
BCLAF1	ENCODE Transcription Factor Targets	1.0	null
liver_a	HPA Tissue Sample Gene Expression Profiles	-1.0	-0.988873
Perturb_15422_KD_PXN_SRP199368	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_3142_OE_CXADR_SRP274008	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.3539
GSE178340_7_v_2_carfilzomib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
periventricular stratum of Str	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.52511
STAT3_MCF 10A_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_Panc1_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
FOXP2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.3146
Perturb_8704_KD_SIRT1_SRP267968	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.5536
Perturb_6100_KD_ZNF622_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE110178_1_v_3_tranylcypromine_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
CEBPB_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15534_KD_YAP1/WWTR1_SRP365715	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_2072_KD_BMAL1_SRP041298	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.21574
GTEX-TMMY-0926-SM-33HBG	GTEx Tissue Sample Gene Expression Profiles	1.0	1.13246
NCI-H2052	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38117
Perturb_569_KD_CYGB_ERP113118	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.60859
H3K4me3_H7_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
BICR22	DepMap CRISPR Gene Dependency	1.0	4.35007
H3K4me1_myotube_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
layer 2 of PCx	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.69193
Perturb_6043_KD_NCOA5_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	14.6729
Lung squamous cell carcinoma_LUSC_TCGA-39-5037-01A-01R-1443-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Alanine aminotransferase levels	GWAS Catalog SNP-Phenotype Associations 2025	1.0	1.30969
CTCF_GM12871_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
tonsil	HPA Tissue Gene Expression Profiles	1.0	1.05162
Perturb_1371_KD_IGF2BP2_SRP252209	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_11949_KD_NRF2_SRP092641	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
MYC_K562_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NFKB1-27076634-BEAS2B-HUMAN-LUNG-INFLAMMATION	ChEA Transcription Factor Targets 2022	1.0	null
EZH2_keratinocyte_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me2_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_ECC-1_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
A-431	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.02175
Triple-Negative Breast Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
GSE120370_0_v_3_thrombin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
H3K27ac_placenta_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_14586_KD_IGF2BP1_SRP291710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.95521
Perturb_2689_KD_BMOR_SRP344304	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
pineal_night	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-0.834332
Perturb_14127_KO_TP53/CDKN2A/PTEN/NF1_SRP258861	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	10.2856
GSE181513_2_v_1_usp7_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE186005_1_v_2_klf5_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
POU3F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4178
YY1_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15220_KD_RACK1_SRP330756	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.0035
NCIH69	CCLE Cell Line Gene CNV Profiles	-1.0	-1.52443
GSE135350_3_v_1_dexamethasone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_2516_KD_YAP1_SRP181909	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.91848
NLRP1 inflammasome complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.005
abnormal germ layer development	MGI Mouse Phenotype Associations 2023	1.0	null
SK-N-BE(2) cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.65
primary visual cortex (striate cortex, area V1/17)_4 mos_M_12296	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.10016
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-EX-A1H5-01A-31R-A13Y-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GR-ST	COSMIC Cell Line Gene Mutation Profiles	1.0	null
ZBTB7A	ENCODE Transcription Factor Targets	1.0	null
GSE195568_6_v_10_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
AF4-26711339-SEM-HUMAN-BLOOD-LEUKEMIA	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_10008_KD_HNRNPU_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.47333
Perturb_1385_KD_Zcchc8_SRP187429	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-7.912
H3K4me3_endothelial cell of umbilical vein_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
POLR2AphosphoS5_HL-60_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CNOT3	ChEA Transcription Factor Targets	1.0	null
SRF	JASPAR Predicted Transcription Factor Targets	1.0	null
SNU-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	1.57666
GSE218907_3_v_2_opa1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE231648_1_v_2_lsm14b_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE198254_1_v_0_metformin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
Perturb_6754_KD_UPF2_SRP327782	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.7283
FOXS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.4572
Perturb_13496_KD_IGF2BP1_SRP252425	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-14.7292
intermediate stratum of JcPV	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.26416
Prostate adenocarcinoma_PRAD_TCGA-KK-A6E1-01A-11R-A311-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
BACH1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXM1_MCF-7_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Low Density Lipoprotein Cholesterol Measurement	DisGeNET Gene-Phenotype Associations	1.0	null
Perturb_9094_KD_SMARCA4_SRP293297	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.10736
GSE128730_3_v_5_neratinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
negative regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
Kidney Chromophobe_KICH_TCGA-KO-8404-01A-11R-2315-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HCFC1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
YY1-26981420-C2C12-MOUSE-MUSCLE	ChEA Transcription Factor Targets 2022	1.0	null
KMT5B	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.11108
JUND_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF558	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	181.806
H2BK5ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
H3K27ac_cortical plate_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
layer 3 of RSC	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.72406
Perturb_15526_KD_CPT1A_SRP292168	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.64702
GSE155162,GSE155169_1_v_2_buparlisib_human	RummaGEO Drug Perturbation Signatures	1.0	null
MAZ_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE149035_2_v_0_hepacam_human	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K4me3_Caco-2_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
TAL1	ENCODE Transcription Factor Targets	1.0	null
GTEX-PVOW-0011-R3A-SM-32PKX	GTEx Tissue Sample Gene Expression Profiles	1.0	0.980202
Perturb_14125_KO_TP53/CDKN2A_SRP258861	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.37888
CTCF_SK-N-SH_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
BHLHE40	ENCODE Transcription Factor Targets	1.0	null
GSE188382_2_v_1_sirt5_human	RummaGEO Gene Perturbation Signatures	1.0	null
Pharyngeal cancer cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.981
H3K4me1_megakaryocyte_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
SK-N-AS	Sanger Dependency Map Cancer Cell Line Proteomics	1.0	1.645
GSE58724_3_v_0_oxymetholone_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
KYAE1	DepMap CRISPR Gene Dependency	1.0	5.41771
GSE98898_7_v_1_hoxa1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
ubiquitin protein ligase activity	GO Molecular Function Annotations 2023	1.0	null
GSE179531_1_v_0_metformin_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE164874_5_v_9_prednisolone_human	RummaGEO Drug Perturbation Signatures	1.0	null
Cervix disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.469
GSE216043_3_v_9_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_14093_KD_HDAC1_SRP199194	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.03025
GSE206516,GSE206518_0_v_7_ptdss2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE226249_2_v_6_pirfenidone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
USF1_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_3736_KD_TMED9_SRP180007	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.11362
CHD1	ENCODE Transcription Factor Targets	1.0	null
Perturb_13949_KD_CDK4/CDK6_SRP258989	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.38857
hsa-miR-548m	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.55165
Perturb_439_KD_MEP50_SRP073189	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	9.02854
Kidney renal clear cell carcinoma_KIRC_TCGA-BP-5004-01A-01R-1334-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
HNT-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.895831
Perturb_15515_KD_E2F2_SRP314859	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.25813
GSE178714_5_v_7_smad2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Perturb_17530_KO_TET1_SRP150212	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.5126
Perturb_970_OE_SRSF1_SRP174924	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.69353
Perturb_13373_KD_RPRD1B_SRP362755	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.18856
A388	COSMIC Cell Line Gene CNV Profiles	1.0	2.39327
Perturb_2762_KD_BRG1_SRP077334	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.82172
Kidney renal papillary cell carcinoma_KIRP_TCGA-GL-7966-01A-11R-2204-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_163_KD_RAC1_SRP387923	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-16.4868
Kidney renal clear cell carcinoma_KIRC_TCGA-B8-4154-01A-01R-1188-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
inferolateral temporal cortex (area TEv, area 20)_8 pcw_M_13058	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	1.0	1.00966
GTEX-Q2AG-0011-R1A-SM-2HMJI	GTEx Tissue Sample Gene Expression Profiles	1.0	1.36647
GSE160817_0_v_1_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Intergeniculate leaflet of the lateral geniculate complex	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.45888
PMC8283158-mmc2.xlsx-TCF4_ChIP-symbol_TCF4	Rummagene Transcription Factor Associations 2026	1.0	null
GSE195559_8_v_5_notch1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
YY1_SK-N-SH_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K27ac_astrocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_GM19099_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2720_KD_YAP1/WWTR1_SRP115100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.388
GTEX-OHPN-0011-R9A-SM-4DXUH	GTEx Tissue Sample Gene Expression Profiles	1.0	1.33452
MYC-19079543-MESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
LB771HNC	DepMap CRISPR Gene Dependency	1.0	3.3767
ETS1_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.01112
GTEX-QDT8-0011-R5A-SM-32PKN	GTEx Tissue Sample Gene Expression Profiles	1.0	1.44286
EN	COSMIC Cell Line Gene Mutation Profiles	1.0	null
GTEX-N7MT-0011-R3a-SM-2I3GC	GTEx Tissue Sample Gene Expression Profiles	1.0	1.7177
Perturb_6101_KD_ZNF638_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me3_fibroblast of skin of abdomen_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Liver hepatocellular carcinoma_LIHC_TCGA-CC-A8HV-01A-11R-A36F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
cingulum bundle, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	2.8288
POU2F2	ENCODE Transcription Factor Targets	1.0	null
Liver hepatocellular carcinoma_LIHC_TCGA-CC-5261-01A-01R-A131-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE69869_0_v_1_panobinostat_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
NIHOVCAR3	CCLE Cell Line Gene CNV Profiles	1.0	1.50009
GTEX-XOTO-0011-R9A-SM-4GICI	GTEx Tissue Sample Gene Expression Profiles	1.0	0.961827
Perturb_3515_KD_EIF4A3_ERP130710	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.81032
GSE154074_2_v_0_bleomycin_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
6071_PARK7_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.627945
GSE88819_1_v_8_tug1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE124375_13_v_0_chd2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Epididymis	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
GSE147662_3_v_1_nicotinamide_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
H3K4me3_CD14-positive monocyte_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
POLR2A_GM12878_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_15452_KD_circCSNK1G3_SRP139940	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.76092
GSE119564_2_v_3_zfp217_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-CJ-4637-01A-02R-1325-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GABPA_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-RU72-0011-R6A-SM-2TF71	GTEx Tissue Sample Gene Expression Profiles	1.0	1.37136
Perturb_46_OE_ERG/MYC_SRP069177	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.30447
skeletalmuscle_d	HPA Tissue Sample Gene Expression Profiles	-1.0	-1.32191
H4K91ac_H1	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
K2	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-5.59724
Head and Neck squamous cell carcinoma_HNSC_TCGA-CR-7404-01A-11R-2132-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
YMB-1-E	COSMIC Cell Line Gene Mutation Profiles	1.0	null
CTCF_MCF-7_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Ovary epithelial cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.06
ZNF384_ES-E14_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2708_KD_RPL7_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.60089
Y-79 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.902
Androgen insensitivity syndrome_Fibroblast_GSE3871	GEO Signatures of Differentially Expressed Genes for Diseases	-1.0	-2.38589
Thyroid	GTEx Tissue Gene Expression Profiles 2023	1.0	5.07952
Gastrointestinal system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.888
CTCF_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
hsa-miR-499-5p	TargetScan Predicted Conserved microRNA Targets	1.0	0.454769
KRAP_Deficiency_GDS3527_566_mouse_Brown adipose tissues	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
GTEX-Q2AG-0011-R8A-SM-2HMK5	GTEx Tissue Sample Gene Expression Profiles	1.0	0.880976
Pheochromocytoma and Paraganglioma_PCPG_TCGA-QR-A70P-01A-11R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
SMIM7	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.45597
GSE126345_9_v_10_hcrt_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
NB-1 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.378
GTF2F1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14188_OE_BCL7A_SRP258290	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.14778
Central nervous system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.552
H2AFZ_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ChIP_H3K36me3_18692474_mouseESC	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
H3K27ac_olfactory bulb_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
GTEX-XMD1-0011-R3B-SM-4AT5R	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09651
SK-MEL-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.19094
H3K23ac_H9	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_15561_KO_SLFN11_SRP327912	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.79511
reticular formation of CoPD	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.2166
emboliform nucleus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.824635
Kidney renal papillary cell carcinoma_KIRP_TCGA-A4-7287-01A-11R-2139-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
negative regulation of signaling	GO Biological Process Annotations 2015	1.0	null
NCIH1755	CCLE Cell Line Gene CNV Profiles	-1.0	-1.32104
Perturb_13733_KD_RUVBL1_SRP126055	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.13012
Perturb_15734_KO_Kmt2d_SRP058264	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-1.90025
CTCF_epithelial cell of esophagus_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
promote	GeneRIF Biological Term Annotations	1.0	null
GTEX-QVJO-0011-R1A-SM-2S1QI	GTEx Tissue Sample Gene Expression Profiles	1.0	1.08641
intracellular part	GO Cellular Component Annotations 2015	1.0	null
Equatorial cell cortex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.655
hsa-miR-4536	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.880544
H3K27ac_fibroblast of lung_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
HDAC2_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_2729_KD_BCL11A_SRP258724	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	17.109
Perturb_6409_OE_ESR2_SRP165889	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-9.20544
USF1	ENCODE Transcription Factor Targets	1.0	null
624 MEL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.836918
GSE102505_6_v_3_tunicamycin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_7821_Mut_BAZ1A_SRP100570	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-10.3529
HCC2998	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Cycling basal cell_Trachea_Mouse	CellMarker Gene-Cell Type Associations	1.0	null
Perturb_8434_KD_CCT3_ERP124101	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.58021
hsa-miR-4680-5p	TargetScan Predicted Conserved microRNA Targets	1.0	0.766596
pineal_day	BioGPS Human Cell Type and Tissue Gene Expression Profiles	-1.0	-0.896751
GSE206516,GSE206518_1_v_4_ptdss2_human	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_11575_OE_YAP_SRP273175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.85944
ChIP_MYC_19079543	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
hsa-miR-3619-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
NEUROG2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.6297
Perturb_5399_KD_RORB_SRP348097	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.20632
GSE226249_5_v_6_pirfenidone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE186440,GSE186443_3_v_7_daxx_human	RummaGEO Gene Perturbation Signatures	-1.0	null
EP300_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
nucleus of Darkschewitsch, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	0.825408
Prostate cancer	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
TBP	ENCODE Transcription Factor Targets	1.0	null
Ebolavirus(ZEBOV)_6day_PBMCs_rhAPCtreated_21987740_GSE24943	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-0.006274
Perturb_8057_KD_IGF2BP3_SRP094100	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.9192
CTCF_fibroblast of villous mesenchyme_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_GM06990_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE195568_6_v_0_palbociclib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Kidney renal clear cell carcinoma_KIRC_TCGA-CW-6097-01A-11R-1672-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
GSE48812_0_v_1_sulforaphane_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Perturb_15701_KO_BNC2_SRP327109	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.4569
Perturb_10246_OE_RUNX1_SRP228597	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
posteroventral (inferior) parietal cortex_30 yrs_F_12290	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-0.883582
PMC9561884__F5	PFOCR Pathway Figure Associations 2024	1.0	null
RAD21	ENCODE Transcription Factor Targets	1.0	null
preweaning lethality, incomplete penetrance	MGI Mouse Phenotype Associations 2023	1.0	null
Perturb_8290_KD_PRPF8_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.5437
Perturb_10733_OE_Sirt6_SRP282071	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	-1.0	-17.8447
GSE155567_2_v_0_cd33_human	RummaGEO Gene Perturbation Signatures	-1.0	null
PMC6904118-NIHMS1544763-supplement-5.xlsx-MYB_Individual-MYB_sgRNA-5_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_8130_KD_DDX6_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-11.4296
Perturb_6016_KD_GATAD2A_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K4me3_G1E_mm9_2	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_9166_KD_circRAB3IP_SRP366297	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-13.1616
GSE110268_2_v_3_foxd1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
rostral ventral respiratory cell group	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.59572
Brain Lower Grade Glioma_LGG_TCGA-HT-A4DV-01A-11R-A26U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
cervix, uterine	HPA Tissue Protein Expression Profiles	-1.0	-1.44043
Perturb_13656_KO_TERT_SRP291201	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.94447
RUNX3_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SNU-484	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.832028
H3K4me3_K562_hg19_3	ENCODE Histone Modification Site Profiles	1.0	null
GSE144443_0_v_1_nicotinamide_mouse	RummaGEO Drug Perturbation Signatures	1.0	null
496100416_FWM_dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.51837
OB glomerular layer	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.31354
intermediate part of the arcuate nucleus	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-2.12726
UACC812	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	-1.0	-0.925781
GSE176093_2_v_3_mineral oil_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
laterorostral part of entorhinal cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-1.16388
animal	TISSUES Experimental Tissue Protein Expression Evidence Scores	1.0	1.53602
GSE135030_8_v_9_fludarabine_human	RummaGEO Drug Perturbation Signatures	1.0	null
GTEX-WHSE-0011-R5A-SM-3P5ZO	GTEx Tissue Sample Gene Expression Profiles	1.0	0.933073
nfe2l2_18059474_liver_lof_mouse_gpl1261_gds3406	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.059563
PMC4224449-pone.0112193.s009.xlsx-PPI_MODULES_CLEAN_MAP_merg_OUT-Symbol_TCF23	Rummagene Transcription Factor Associations 2026	1.0	null
dorsolateral prefrontal cortex_1 yrs_F_12830	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.14615
Rectum adenocarcinoma_READ_TCGA-DC-4745-01A-01R-A32Z-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
POLR2A_MCF 10A_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Infertility, Male	CTD Gene-Disease Associations	1.0	1.14098
H3K9ac_Stomach Smooth Muscle	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
CTCF_A549_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF143_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE227592_10_v_3_adar_human	RummaGEO Gene Perturbation Signatures	-1.0	null
496100352_FWM_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.27497
Corpus callosum	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.3
Pancreatic Carcinoma	DisGeNET Gene-Disease Associations	1.0	null
HT-115	COSMIC Cell Line Gene Mutation Profiles	1.0	null
MYC_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_7241_KD_UPF1LL_SRP295982	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.33445
H3K4me3_G1E-ER4_mm9_3	ENCODE Histone Modification Site Profiles	1.0	null
TEAD4_H1-hESC_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-Q2AG-2926-SM-2HMJ3	GTEx Tissue Sample Gene Expression Profiles	1.0	1.18014
Perturb_9087_KD_SSRP1_SRP106869	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.57519
FOXA3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.2318
GSE202434,GSE202438_6_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	1.0	null
TCF7L2_Panc1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
intermediate stratum of Pal	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.0447
10623_ZNF774_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	-1.0	-0.630921
2376_DROSHA_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.618907
FOS_MCF 10A_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
E2F6_K562_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ZNF652	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.007
YY1_K562_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
MAFF_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
HCC2688	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.03096
MAFK	ENCODE Transcription Factor Targets	1.0	null
NCIH2170	CCLE Cell Line Gene CNV Profiles	-1.0	-1.352
GSE166004_3_v_2_pld1_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE179880_8_v_5_e2f4_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GSE139540_0_v_1_menadione_human	RummaGEO Drug Perturbation Signatures	-1.0	null
BHLHE22	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.7895
r2 part of basomedial reticular formation	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	2.05743
Adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.593
Perturb_8123_KD_U2AF2_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.71496
GSE184884_7_v_1_gps2_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
POLR2A_A549_hg19_5	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_fibroblast of upper leg skin_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
ZNF384_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14236_KO_Tet2_SRP237910	PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations	1.0	20.0
Cholangiocarcinoma cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.946
E2F4_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
inferolateral temporal cortex (area TEv, area 20)_37 pcw_M_263195015	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-1.43739
GSE201270,GSE201272_5_v_1_mybl2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
SIN3A_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
PMC7753765__F3	PFOCR Pathway Figure Associations 2024	1.0	null
H3K4me1_G1E-ER4_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Esophageal cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.269
Sarcoma_SARC_TCGA-KD-A5QU-01A-11R-A27Q-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Reproductive organ cancer	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	1.0	0.638
Lung adenocarcinoma_LUAD_TCGA-53-7624-01A-11R-2066-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
hsa-miR-28-3p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.7397
H3K4me1_cerebellum_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_11935_KD_mir3783p_SRP321149	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-3.00949
degradation	GeneRIF Biological Term Annotations	1.0	null
Perturb_8354_KD_PtenTraf3_SRP337419	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.11695
GSE119978,GSE180930_0_v_1_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
periventricular stratum of Pal	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.63453
PMC8755441-mmc3.xlsx-IRF7-Up-ezh2_IRF7	Rummagene Transcription Factor Associations 2026	1.0	null
Mesothelioma_MESO_TCGA-MQ-A4LM-01A-11R-A34F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Presubiculum, layer 3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.37926
Hepatocellular carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.636
Perturb_6642_KO_ZNF519_SRP371738	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.3203
PMC11947124-41419_2025_7562_MOESM1_ESM.docx-63-ZNF358_ZNF358	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_5999_KD_CBX3_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Monogenic disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.091
MDAMB231	CCLE Cell Line Gene CNV Profiles	-1.0	-1.32354
CTCF_MCF-7_hg19_7	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE140651,GSE140653_2_v_6_med1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Sarcoma_SARC_TCGA-QQ-A5VB-01A-11R-A36F-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_1370_KD_IGF2BP1_SRP252209	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-7.7022
GSE48812_0_v_5_sulforaphane_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE160246_9_v_5_cpeb4_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.987652
CTCF_GM12878_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_GM12865_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_spleen_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SLC33A1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.27625
RVH-421	COSMIC Cell Line Gene Mutation Profiles	1.0	null
Lung squamous cell carcinoma_LUSC_TCGA-66-2737-01A-01R-0980-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
anterior (rostral) cingulate (medial prefrontal) cortex_36 yrs_M_12302	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	-1.0	-2.6111
GTEX-OXRO-0011-R9A-SM-3NB1X	GTEx Tissue Sample Gene Expression Profiles	1.0	1.09924
Perturb_9908_KD_GRSF1_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-8.07556
ZC3H11A	ENCODE Transcription Factor Targets	1.0	null
mantle zone of SePal	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.33743
PMC10363146-41598_2023_38681_MOESM1_ESM.pdf-509-ELF4_ELF4	Rummagene Transcription Factor Associations 2026	1.0	null
Perturb_289_KO_PHF8_SRP399627	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.80998
HCC1187	Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles	-1.0	-1.23249
RCOR1_IMR-90_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE160817_5_v_6_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
pallidohypothalamic nucleus, left	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.04569
Perturb_18442_KD_YAP1/WWTR1_SRP303519	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-6.04766
GSE173232_4_v_3_sf3b1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Cortical amygdalar area, posterior part, lateral zone	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.05566
HCC12	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-0.988609
NCI-H1836	COSMIC Cell Line Gene Mutation Profiles	1.0	null
JNK_KO_GDS3001_531_mouse_liver	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
Perturb_2318_KD_PRPF8_SRP268983	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.35018
Drug-Induced Liver Injury	CTD Gene-Disease Associations	1.0	1.62423
E2F4	ENCODE Transcription Factor Targets	1.0	null
GSE174498,GSE174500_0_v_8_asparaginase_human	RummaGEO Drug Perturbation Signatures	1.0	null
ELK1_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXM1-26456572-MCF-7-HUMAN-BREASTCANCER	ChEA Transcription Factor Targets 2022	1.0	null
GTEX-N7MS-0011-R8a-SM-2YUMK	GTEx Tissue Sample Gene Expression Profiles	1.0	2.01604
hsa-miR-195	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
A-Vietnam-1203-2004(H5N1)_24Hour_None_GSE43204	GEO Signatures of Differentially Expressed Genes for Viral Infections	-1.0	-1.48206
U-937	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.07305
H3K4me3_HL-60_hg19_2	ENCODE Histone Modification Site Profiles	1.0	null
FOXA1_T47D_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SW579	DepMap CRISPR Gene Dependency	1.0	4.68043
Kidney renal clear cell carcinoma_KIRC_TCGA-CZ-4858-01A-01R-1305-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
NCI-H889	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	-1.0	-1.73234
Perturb_6030_KD_LLPH_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Primary motor area, Layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.22398
H3K4me3_NT2-D1_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
FOXP2_PFSK-1_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CTCF_fibroblast of foreskin _hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE112762,GSE112767_2_v_0_dgcr8_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
H3K27ac_MEL cell line_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_14178_KO_CD33/CD123_SRP387539	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Anteromedial visual area, layer 2/3	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.25945
Perturb_11382_KD_NKX25_SRP152523	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
3086_FIP1L1_P1P2	Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures	1.0	0.619386
placenta	HPA Tissue Protein Expression Profiles	1.0	1.24946
Zinc finger, B-box	InterPro Predicted Protein Domain Annotations	1.0	null
GSE123825_2_v_3_glutamine_mouse	RummaGEO Drug Perturbation Signatures	-1.0	null
Orbital area, ventrolateral part	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.13989
Perturb_14116_KD_RPS6KB1_SRP187713	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.96526
H3K4me2_CH12.LX_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_2578_KD_BAZ1B_ERP133231	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.3564
membrane part	GO Cellular Component Annotations 2015	1.0	null
POLR2AphosphoS2_CH12.LX_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
SNRPG	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.05876
H3K27ac_H1 Derived Neuronal Progenitor Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_17639_OE_WWTR1_SRP298391	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
Liver hepatocellular carcinoma_LIHC_TCGA-CC-A3MA-01A-11R-A213-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_6097_KD_ZNF438_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	15.7067
KP-2	Sanger Dependency Map Cancer Cell Line Proteomics	-1.0	-2.31597
VZ in ventromedial extrastriate cortex (VP)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	0.853771
Pheochromocytoma and Paraganglioma_PCPG_TCGA-WB-A81Q-01A-11R-A35L-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
ventral posterior inferior nucleus	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	-1.0	-0.964728
Pheochromocytoma and Paraganglioma_PCPG_TCGA-RW-A68F-01A-11R-A35K-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
FOXA2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.3974
HOXB7	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.46379
Cervical squamous cell carcinoma and endocervical adenocarcinoma_CESC_TCGA-EK-A2RL-01A-11R-A18M-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_11373_KD_USP22_SRP229365	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	8.31532
Perturb_7873_KD_FSCN1_SRP258738	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	3.98707
Perturb_12256_KO_CD274_SRP215305	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	13.4926
Perturb_13873_KD_ELF4_SRP182698	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
Perturb_14576_KO_NQO1_SRP217327	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.34166
POLR2A_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-FG-5963-01A-11R-1708-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
TEAD1	JASPAR Predicted Transcription Factor Targets	1.0	null
Perturb_2759_KD_BRG1_SRP077334	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	4.76526
EZH2	ENCODE Transcription Factor Targets	1.0	null
Perturb_15344_KD_PGR_SRP223388	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.33568
reticular nucleus of thalamus, right	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	1.0	1.68245
hsa-miR-891b	TargetScan Predicted Conserved microRNA Targets	1.0	0.632343
H3K4me3_H1-hESC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
PMC7371429-elife-53600-supp2.xlsx-annotated_MEIS1_in_B13ko-M1-Nearest_Ensembl_MEIS1	Rummagene Transcription Factor Associations 2026	1.0	null
H3K4me1_CD14-positive monocyte_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
Perturb_12730_KD_INCA1_SRP221667	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.82209
Perturb_6033_KD_LTBP2_SRP271175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
GSE190384,GSE190386_0_v_8_fulvestrant_human	RummaGEO Drug Perturbation Signatures	-1.0	null
RBBP5_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GTEX-XYKS-0526-SM-4BRW2	GTEx Tissue Sample Gene Expression Profiles	1.0	1.05814
Perturb_2770_KD_HOXA11_SRP072302	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
hsa-miR-3065-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.880544
15260889-TableS2a	GeneSigDB Published Gene Signatures	1.0	null
outer SZ in primary visual cortex	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.49673
FOS_01_99	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.5976
Perturb_8197_KD_TRIM56_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
marc145	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.305
POLR2AphosphoS5_SK-N-SH_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE102505_5_v_0_tunicamycin_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE235587_2_v_0_mitoxantrone_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC9574515-mmc2.xls-THP1_60_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
ELK1_HeLa-S3_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CHD2	ENCODE Transcription Factor Targets	1.0	null
H3K27ac_HeLa-S3_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
GSE160817_0_v_6_slamf6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
TAF1_HeLa-S3_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
FOXA1	ENCODE Transcription Factor Targets	1.0	null
Brain Lower Grade Glioma_LGG_TCGA-FG-A87Q-01A-11R-A36H-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Perturb_13922_KO_PPARGC1A_SRP314654	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-12.3921
Perturb_14577_KO_NQO1_SRP217327	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.63273
TBP_MEL cell line_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
lymph node	HPA Tissue Gene Expression Profiles	1.0	1.12357
Head and Neck squamous cell carcinoma_HNSC_TCGA-CN-A6V7-01A-12R-A34R-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Orbital area, ventrolateral part, layer 1	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	-1.0	-1.42215
GSE142210_4_v_6_panobinostat_human	RummaGEO Drug Perturbation Signatures	-1.0	null
GSE255680_2_v_3_igf2_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
Perturb_5634_KD_FLI1_SRP142503	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-1.48739
TAF1_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
cytoplasmic part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
Perturb_2347_KD_ELP3_ERP122258	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.3273
NCI-H810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles	1.0	0.982591
Bladder Urothelial Carcinoma_BLCA_TCGA-CU-A0YR-01A-12R-A10U-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Retinal disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.082
GSE178340_5_v_2_carfilzomib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
POLR2A_myocyte_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Perturb_14148_KO_KBTBD4_SRP279638	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	6.29813
Perturb_8300_KD_AUH_SRP013565	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-5.91217
Perturb_93_KD_ANXA4_SRP127547	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-4.68674
TAL1_MEL cell line_mm9_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GSE174498,GSE174500_3_v_1_asparaginase_human	RummaGEO Drug Perturbation Signatures	-1.0	null
Skin Cutaneous Melanoma_SKCM_TCGA-FS-A1Z4-06A-11R-A18T-07	TCGA Signatures of Differentially Expressed Genes for Tumors	1.0	null
Lung disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.934
H3K4me1_endothelial cell of umbilical vein_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
NFYB_GM12878_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
GATA2_01_193	KnockTF Gene Expression Profiles with Transcription Factor Perturbations	-1.0	-0.58518
Perturb_15559_KO_SLFN11_SRP327912	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-20.0
layer 6 of PaS	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	1.0	1.97914
GSE136894_1_v_0_psen1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE202434,GSE202438_4_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PMC11161988-12906_2024_4523_MOESM3_ESM.pdf-97-SOX14_SOX14	Rummagene Transcription Factor Associations 2026	1.0	null
VZ in caudal midinferior temporal cortex (area TF)	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	1.0	1.30748
CTCF_HeLa-S3_hg19_4	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_spleen_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_erythroblast_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
Hepatomegaly	CTD Gene-Disease Associations	1.0	1.28858
FGFR3_KD_GDS4454_78_human_RT112	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	null
Perturb_8848_KD_APC_SRP267478	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	20.0
H3K36me3_ES-E14_mm9_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
fat_e	HPA Tissue Sample Gene Expression Profiles	-1.0	-0.83743
5732_NOL10_P1P2	Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures	1.0	0.539405
H3K27ac_testis_mm9_1	ENCODE Histone Modification Site Profiles	1.0	null
HDAC2_H1-hESC_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
H3K4me3_CD4+ CD25int CD127+ Tmem Primary Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
GSE109530,GSE109531_1_v_3_hdac3_mouse	RummaGEO Gene Perturbation Signatures	1.0	null
GTEX-R55E-0011-R4A-SM-2TC5H	GTEx Tissue Sample Gene Expression Profiles	1.0	0.95173
Perturb_2836_KD_MDC1_SRP313175	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-2.81167
H3K4me1_H1-hESC_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
H3K4me3_H1 BMP4 Derived Trophoblast Cultured Cells	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_9814_KD_TAL1_SRP062773	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	-17.5686
PMC9530161-41419_2022_5296_MOESM2_ESM.xlsx-Tab10_KDM5C-KD-up-DKD-rescued-Table_10_Up-regulated_genes_in_KDM5C-KD_and_rescued_genes_in_DKD_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Fedratinib (hydrochloride hydrate)_NCI-H23	Tahoe Therapeutics Tahoe 100M Perturbation Atlas	-1.0	-0.0156302
GSE202434,GSE202438_4_v_1_talazoparib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
POLR2A_K562_hg19_7	ENCODE Transcription Factor Binding Site Profiles	1.0	null
X, left, lateral hemisphere	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	-1.0	-1.20718
H3K4me3_iPS DF 19.11	Roadmap Epigenomics Histone Modification Site Profiles	1.0	null
Perturb_15108_KD_MPP8_SRP218207	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	2.61466
GSE110268_0_v_3_foxd1_mouse	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE188458_2_v_4_hydrogen peroxide_human	RummaGEO Drug Perturbation Signatures	-1.0	null