association	dataset	threshold value	standardized value
KAP1-22055183-ESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
VMRC-LCD	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	3.19301
GSE77108_4_v_2_saha_human	RummaGEO Drug Perturbation Signatures	1.0	null
NR3C1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.9789
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.8717
COLO 857	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.07468
POU3F3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.5182
REST_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCIH69	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65515
ONECUT1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	41.5324
Ar	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	34.6316
KARPAS620	CCLE Cell Line Gene CNV Profiles	-1.0	-1.35362
496100640_PCx_no dementia_no TBI_95-99_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.03359
GABPA	ENCODE Transcription Factor Targets	1.0	null
mRNA_MYOD1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
Atf3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	39.1142
496100497_FWM_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.2501
Hnf1a	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	46.6133
mRNA_NR0B1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
POU2F2	JASPAR Predicted Transcription Factor Targets	1.0	null
GATA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.855
Organ system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.126
PMC5193459-pone.0168968.s009.xlsx-Dharmacon_OTP_siRNA_Area-Symbol_OTP	Rummagene Transcription Factor Associations 2026	1.0	null
PAX5_GM12878_hg19_3	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H920	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.63457
FOXA1	JASPAR Predicted Transcription Factor Targets	1.0	null
GSE240386,GSE242143_8_v_6_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
G130	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32131
Vdr	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	60.8207
FOXC1	JASPAR Predicted Transcription Factor Targets	1.0	null
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.868715
RHOXF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.1647
blood	GTEx Tissue Gene Expression Profiles	1.0	0.865776
DUX4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	41.5931
PITX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.385
Arid5a	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	27.6635
CTCF_T-cell acute lymphoblastic leukemia_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
ion binding	GO Molecular Function Annotations 2015	1.0	null
Intestinal cancer cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.652
hsa-miR-4703-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
NCIH2052	CCLE Cell Line Gene CNV Profiles	1.0	1.85047
KYSE-140	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60249
Prdm15	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	34.8619
496100462_PCx_dementia_TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.24213
MPP89	CCLE Cell Line Gene CNV Profiles	-1.0	-1.79456
ZR-75-30	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.870657
HS 578T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.993533
Hoxa13	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.3141
bcor_22012066_cn_aml_lof_human_gpl570_gds4280	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.098073
SRY	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.8571
SNRPG	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-3.3201
B30.2/SPRY domain	InterPro Predicted Protein Domain Annotations	1.0	null
FOSL2	ENCODE Transcription Factor Targets	1.0	null
hsa-miR-3942-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
Hmx1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	39.5389
NCIH1623	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37144
GSE163240_3_v_4_enzalutamide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
HNF1A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	55.1046
mRNA_ASCL2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
Intestinal cancer cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.573
HULC complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.788
ubiquitin protein ligase activity	GO Molecular Function Annotations 2025	1.0	null
Nanog	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	32.4526
Shu complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.927
organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
MYCN-27167114-CHIP-SEQ-NEUROBLASTOMA-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
MutLalpha complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.666
LNCAP	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.972687
POU2F1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.1581
Nfatc2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	30.168
DMS 53	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.78134
ubiquitin-protein transferase activity	GO Molecular Function Annotations 2025	1.0	null
Large intestine cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.342
PMC10335677-pbio.3002161.s009.xls-MLL_siRNA_DEGs-Ensembl_Symbol_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
MKN-74	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.3036
496100364_TCx_possible Alzheimer's disease_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.36678
Pax7	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	47.3813
Intestinal disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.249
BEN	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.28247
NR3C1-21868756-MCF10A-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
SMAD4-21799915-A2780-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Perturb_307_KD_TPRX1/TPRX2_SRP361145	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	1.35457
Esophagus - Gastroesophageal Junction	GTEx Tissue Gene Expression Profiles 2023	1.0	7.21239
mRNA_SALL4_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
LP1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.88228
FOXC2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	80.2896
Nkx3-1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	35.1
NCI-H1869	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.972687
SNU-C5	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.961
POU3F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.565
MEIS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.8222
496100539_HIP_probable Alzheimer's disease_TBI_78_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	4.13578
NR2F1	JASPAR Predicted Transcription Factor Targets	1.0	null
PMC10800016-table_s3_20230913_ddad186.xlsx-DUX4-aff_I-Unnamed_1_DUX4	Rummagene Transcription Factor Associations 2026	1.0	null
NCI-H2172	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14529
Nfatc1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	31.3103
NDUFA1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.01001
Concanavalin A-like lectin/glucanase domain	InterPro Predicted Protein Domain Annotations	1.0	null
protein ubiquitination	GO Biological Process Annotations 2023	1.0	null
Shox2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.0627
JHOM1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.75264
SOX8	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.3511
SW 1417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.20297
Cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.1
ELF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.6675
molecular_function	GO Molecular Function Annotations 2015	1.0	null
GSE235066_7_v_0_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.25364
G-402	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.60842
POU3F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.7478
FOXH1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.1377
Yy1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.2198
TCC-PAN2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.942526
PROP1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	43.7787
mRNA_NR2F2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
GSE118077_1_v_8_sprr5_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Lhx3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	52.0
IRF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.7252
SMC4-20622854-HELA-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
MEF2D	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	64.4299
mRNA_MYBL2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
T-47D	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.39732
JMSU1	CCLE Cell Line Gene CNV Profiles	1.0	1.37423
Zfp809	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	53.2054
496100533_TCx_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	2.69232
Nr2e1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	25.2528
HCC1143	CCLE Cell Line Gene CNV Profiles	1.0	2.27946
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.0022
ubiquitin-like protein ligase activity	GO Molecular Function Annotations 2023	1.0	null
ETV3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.2119
Foxf1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	43.4313
DPRX	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.4214
HS 766T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.993533
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.901646
LAMA84	CCLE Cell Line Gene CNV Profiles	-1.0	-1.39402
PMC5735185-41467_2017_1200_MOESM4_ESM.xlsx-Table_S1-Choi_et_al_2016_DUX4_up-regulated_targets_DUX4	Rummagene Transcription Factor Associations 2026	1.0	null
Runx1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	18.533
RORB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.4542
Nr1h3::Rxra	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	47.2514
ubiquitin-protein transferase activity	GO Molecular Function Annotations 2023	1.0	null
FOXB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	66.5128
ZIM3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	36.482
OTX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.988
SW 948	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.29912
HSF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.7467
SUM 149PT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.993533
CX-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.941377
GSE216043_7_v_5_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
KATO III	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.37865
LXFL529	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.49997
FOXE1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	193.216
HMY-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.44971
PMC9574515-mmc2.xls-THP1_0_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
Sox3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	17.7826
Six4	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	49.7786
HCC60	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82622
Glutathione synthase complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.623
MEF2A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	80.8612
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.5934
BXPC-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.86967
Disease of cellular proliferation	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.095
mRNA_TCF3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
ELK1::HOXB13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.6336
ZBTB17	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.0638
hsa-miR-3117-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.99187
GSE153871_1_v_3_cytarabine_human	RummaGEO Drug Perturbation Signatures	1.0	null
SNU-C4	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.005
Colonic disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.427
Nr5a2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	45.6021
PMC12171002-jcav16p2578s1.pdf-23-PBX3_PBX3	Rummagene Transcription Factor Associations 2026	1.0	null
HCC1187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.901646
POU2F3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.6777
hsa-miR-3662	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.40969
MutSalpha complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.595
PMC10794847-mmc3.xlsx-PBRM1_KD_down-Table_S2_Differentially_expressed_genes_with_PBRM1_knockdown_in_the_differentiation_state_Related_to_Figure_2_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Dlx4	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	27.3066
Cecum cancer cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.679
SMAD4	ChEA Transcription Factor Targets	1.0	null
OCI-LY-10	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.25045
HOXB13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.0601
Stat5a	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	51.6234
GSE74251_0_v_3_decitabine_human	RummaGEO Drug Perturbation Signatures	1.0	null
TP63-22573176-HFKS-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
NR3C1-21868756-MCF10A-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
H2AFZ	ENCODE Transcription Factor Targets	1.0	null
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.932516
Rhox11	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	17.2323
zinc ion binding	GO Molecular Function Annotations 2015	1.0	null
OCT4-19829295-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Spi1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	117.725
EVSAT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.41593
Gli1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	33.7667
NCI-H1882	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.993533
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.993533
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00105
NCIH23	CCLE Cell Line Gene CNV Profiles	1.0	2.25339
GSE143692_0_v_1_trim8_human	RummaGEO Gene Perturbation Signatures	1.0	null
Sox5	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	25.5323
GSE77108_8_v_2_saha_human	RummaGEO Drug Perturbation Signatures	1.0	null
Tbx6	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	36.3357
mRNA_FEM1B_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
BJAB cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.664
HEP G2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1563
POU2F1::SOX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	36.5634
NR3C1	ChEA Transcription Factor Targets	1.0	null
PITX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.4155
Plagl1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	31.4654
Lef1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	53.3164
regulation of macromolecule metabolic process	GO Biological Process Annotations 2023	1.0	null
decitabine_homo sapiens_gpl570_gse30985	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
M059K	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.41028
membrane-bounded organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
COLO 853	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00221
TCCSUP	CCLE Cell Line Gene CNV Profiles	-1.0	-1.41672
mRNA_NANOG_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
Hoxd13	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	22.6512
PAX5	ENCODE Transcription Factor Targets	1.0	null
mRNA_ZSCAN4C_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
NFIC::TLX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.375
PMC11982601-IMM-175-84-s005.xlsx-Fig5D_LPS-Innate_IRF6	Rummagene Transcription Factor Associations 2026	1.0	null
SW1783	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58701
Glycine cleavage complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.424
JIMT1	CCLE Cell Line Gene CNV Profiles	1.0	2.00825
Ppara	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	16.334
Butyrophylin-like	InterPro Predicted Protein Domain Annotations	1.0	null
ETV6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.0359
FOXL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	37.8496
SPIB	JASPAR Predicted Transcription Factor Targets	1.0	null
Nkx3-2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	46.2809
TEAD1	JASPAR Predicted Transcription Factor Targets	1.0	null
H3K4me2_K562_hg19_1	ENCODE Histone Modification Site Profiles	1.0	null
mRNA_GATA3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
ZNF354A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	144.672
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.08891
SMAD4-21799915-A2780-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
Foxl2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	76.9056
mRNA_DLX3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
cation binding	GO Molecular Function Annotations 2015	1.0	null
GSE138633_2_v_0_bag3_human	RummaGEO Gene Perturbation Signatures	-1.0	null
IRF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	64.4516
HCC2218	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03794
NCI-H2106	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.19544
hsa-miR-4774-3p	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.880544
GSE168401_1_v_3_harmine_human	RummaGEO Drug Perturbation Signatures	1.0	null
hsa-miR-573	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
JIMT-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.04543
DMS454	CCLE Cell Line Gene CNV Profiles	-1.0	-1.60757
TE11	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48676
OLIG1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.7831
GSC	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.1154
PMC8120133-supplementarytables_ddab063.xlsx-Table_S2-Table_S2_Differentially_expressed_genes_in_DUX4-fl_and_DUX4-s_DUX4	Rummagene Transcription Factor Associations 2026	1.0	null
GSE235066_4_v_0_cisplatin_human	RummaGEO Drug Perturbation Signatures	1.0	null
regulation of gene expression	GO Biological Process Annotations 2023	1.0	null
KYSE520	CCLE Cell Line Gene CNV Profiles	-1.0	-1.61047
PBX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	44.9971
cell part	GO Cellular Component Annotations 2015	1.0	null
TEAD4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.6377
Hand1::Tcf3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.4138
Stat6	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	46.9352
HCC1599	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.12665
GSE228106_0_v_4_paclitaxel_human	RummaGEO Drug Perturbation Signatures	1.0	null
Gfi1b	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	59.4764
PSN1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.34615
intracellular membrane-bounded organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
GSE240386,GSE242143_1_v_4_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
GSE195559_8_v_1_notch1_human	RummaGEO Gene Perturbation Signatures	1.0	null
transition metal ion binding	GO Molecular Function Annotations 2015	1.0	null
GSE195559_0_v_1_notch1_human	RummaGEO Gene Perturbation Signatures	1.0	null
hsa-miR-3616-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.942526
SMRT-27268052-CHIP-SEQ-BCELLS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Sox17	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	28.4821
NKX2-8	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.6173
Ikzf3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	38.8825
PMC8046804-41467_2021_22478_MOESM11_ESM.xlsx-Del_AA-TCGA-Unnamed_36_TEAD1	Rummagene Transcription Factor Associations 2026	1.0	null
HOXC13	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.0937
Colon mucinous adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.092
POU5F1B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.7682
mRNA_RHOX6_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
mRNA_EOMES_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
ELK3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.4653
NCIH2106	CCLE Cell Line Gene CNV Profiles	-1.0	-1.75163
IRF5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.6981
Dlx3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	26.8062
GABPA_GM12878_hg19_2	ENCODE Transcription Factor Binding Site Profiles	1.0	null
NCI-H1666	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.941377
IRF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.0971
ubiquitin-like protein ligase activity	GO Molecular Function Annotations 2025	1.0	null
CHAGO-K-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.49997
Nr5a1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	56.8422
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.992473
mRNA_ESX1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
PMC11185762-media-2.xlsx-ATAC2wk_KD_V337M_intersect_peak-Symbol_AR	Rummagene Transcription Factor Associations 2026	1.0	null
Colon cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.44
HS 746T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.3673
PMC6639357-41467_2019_11150_MOESM4_ESM.xlsx-SupTab1_Activated_genes_diffex-Supplementary_Data_1_Fold_change_and_p-value_of_all_activated_protein_coding_genes_upon_DNMT1-KO_DNMT1	Rummagene Transcription Factor Associations 2026	1.0	null
SNU-398	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.78134
OKAJIMA	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.51711
Skeletal Muscle Female	Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles	-1.0	-1.12692
EVSA-T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.47482
RUNX2	ChEA Transcription Factor Targets	1.0	null
Foxo3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	43.74
GSE240386,GSE242143_1_v_6_morc2_human	RummaGEO Gene Perturbation Signatures	1.0	null
DUXA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.8848
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4157
496100426_PCx_no dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	5.21836
NKX2-4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.8986
496100618_PCx_probable Alzheimer's disease_no TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.86268
C3A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.931402
PCI-30	COSMIC Cell Line Gene CNV Profiles	1.0	2.93899
NCI-H2110	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.12665
Dlx5	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	30.348
BT549	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46344
SATB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	40.2375
Gata3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	22.1524
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.86649
Ebf4	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	36.0977
YY1	JASPAR Predicted Transcription Factor Targets	1.0	null
RUNX2-22187159-PCA-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Hand1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	33.3766
GSE163240_3_v_0_enzalutamide_human	RummaGEO Drug Perturbation Signatures	-1.0	null
BRD4-25478319-HGPS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
GSE145639_7_v_4_adar_human	RummaGEO Gene Perturbation Signatures	1.0	null
Sox7	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.6915
POU6F1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.1617
hsa-miR-4766-3p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
Arnt	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	16.05
binding	GO Molecular Function Annotations 2015	1.0	null
OVCAR8	CCLE Cell Line Gene CNV Profiles	1.0	1.58842
PITX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.369
KARPAS-620	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.68663
NCI-H1568	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.868715
Jun	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	24.6711
Arid3a	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	26.2593
Stomach Smooth Muscle	Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles	-1.0	-1.15125
ZNF184	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	3.21935
BEN	CCLE Cell Line Gene CNV Profiles	1.0	1.59451
JL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72749
HCC1143	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.21971
Dux	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	46.9345
FOXD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	209.265
HNF1B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.6035
BICR 78	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.51711
Foxj3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	100.729
CTCF	ENCODE Transcription Factor Targets	1.0	null
mRNA_FOXJ2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
mRNA_CDX2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
GSE195559_8_v_5_notch1_human	RummaGEO Gene Perturbation Signatures	1.0	null
RUNX2	JASPAR Predicted Transcription Factor Targets	1.0	null
GSE115542_2_v_0_digoxin_human	RummaGEO Drug Perturbation Signatures	1.0	null
Stat5a::Stat5b	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	38.1159
PMC12003903-41531_2025_933_MOESM1_ESM.pdf-11-ZNF2_ZNF2	Rummagene Transcription Factor Associations 2026	1.0	null
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.836087
prednisolone_homo sapiens_gpl570_gse32962	GEO Signatures of Differentially Expressed Genes for Small Molecules	-1.0	null
Retinitis pigmentosa 11	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.253
RUNX2-22187159-PCA-HUMAN	ChEA Transcription Factor Binding Site Profiles	1.0	null
FOXC1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	73.0172
Pparg::Rxra	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	34.8595
ONECUT3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	168.91
U-2 OS	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.09019
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.870657
GSE233679_5_v_3_nicotinamide_human	RummaGEO Drug Perturbation Signatures	1.0	null
ECGI10	CCLE Cell Line Gene CNV Profiles	1.0	1.44166
CDX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	45.8935
mRNA_SMAD4_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
VMRCLCD	CCLE Cell Line Gene CNV Profiles	1.0	3.2803
SNU-601	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.901646
Gastrointestinal system disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.109
Zfp335	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	17.4167
hsa-miR-3646	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.809003
Prdm4	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	49.2185
OCI-LY7	COSMIC Cell Line Gene CNV Profiles	1.0	2.93899
Sox1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	19.1913
mRNA_KLF4_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
Arnt::Hif1a	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	14.2212
KU812	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.992473
NCIH2172	CCLE Cell Line Gene CNV Profiles	1.0	1.92717
TTE-1 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.706
Perturb_17333_OE_NANOS1_SRP216951	PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations	1.0	7.00719
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.39732
hsa-miR-561	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.07142
regulation of macromolecule biosynthetic process	GO Biological Process Annotations 2025	1.0	null
Dmrt1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	39.1882
GSE192771_2_v_3_sorafenib_human	RummaGEO Drug Perturbation Signatures	1.0	null
Foxo1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	43.0408
PMC9574515-mmc1.xls-THP1_0_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
H2AFZ_K562_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
CAL851	CCLE Cell Line Gene CNV Profiles	1.0	1.33025
pyrazinamide_mus musculus_gpl6246_gse48027	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
GSE147876,GSE147877_2_v_7_enzalutamide_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE209582_1_v_3_chloroquine_human	RummaGEO Drug Perturbation Signatures	1.0	null
Brush cell (Tuft cell)_Lung_Mouse	CellMarker Gene-Cell Type Associations	1.0	null
GSE111247_0_v_1_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
mRNA_NRIP1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
ELF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.7379
Colon adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.467
GSE172458_0_v_1_cisplatin_human	RummaGEO Drug Perturbation Signatures	-1.0	null
OVMANA	CCLE Cell Line Gene CNV Profiles	1.0	1.41548
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.01448
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.846
MEF2B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	55.5728
JJN-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.39732
Nr2f6	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	49.2408
stomach	GTEx Tissue Gene Expression Profiles	1.0	0.828024
TEAD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1395
BT-483	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.931524
Stat5b	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	32.3801
Intestinal cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.341
Prdm14	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	34.4852
MONOMAC1	CCLE Cell Line Gene CNV Profiles	-1.0	-3.21049
RBPJ-21746931-IB4-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
PHOX2B	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.3696
SNU-423	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.901646
GSE236228_0_v_1_penfluridol_human	RummaGEO Drug Perturbation Signatures	-1.0	null
PAX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5458
cytoplasm	LOCATE Predicted Protein Localization Annotations	1.0	null
Mafg	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.7537
FOXD2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	101.184
Zinc finger, RING-type, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.01448
Gastrointestinal system cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.235
FOXF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.4697
Nfat5	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	40.2584
mRNA_MYC_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
cellular_component	LOCATE Predicted Protein Localization Annotations	1.0	null
Elf5	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	66.5569
Arx	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	19.5267
ubiquitin protein ligase activity	GO Molecular Function Annotations 2023	1.0	null
ZNF768	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.4492
GSE168797_1_v_0_cannabidiol_human	RummaGEO Drug Perturbation Signatures	1.0	null
MAFK	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.7968
KYSE-180	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.17591
KYSE-70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.24661
mRNA_TUBA1A_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
GSE74251_0_v_1_decitabine_human	RummaGEO Drug Perturbation Signatures	1.0	null
Ebf2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	41.3372
Smad4	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	40.094
cellular_component	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.2233
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1396
LN443	CCLE Cell Line Gene CNV Profiles	1.0	2.12003
Colorectal cancer	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.343
Msx3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	29.8066
HS746T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.97704
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.853223
GCIY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51048
KYSE-450	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.929125
PMC10335677-pbio.3002161.s009.xls-MLL_siRNA_DEGs-Ensembl_ID_KMT2A	Rummagene Transcription Factor Associations 2026	1.0	null
PMC5446900-NIHMS72240-supplement-Table_S1.xlsx-Table_S1-Table_S1_Genes_differentially_expressed_in_human_primary_myoblasts_upon_ectopic_expression_of_DUX4_DUX4	Rummagene Transcription Factor Associations 2026	1.0	null
BCOR-27268052-CHIP-SEQ-BCELLS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Sox6	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	49.9036
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.09019
NCI-H1623	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32131
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.25045
NCI-H1092	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60249
Zinc finger, RING/FYVE/PHD-type	InterPro Predicted Protein Domain Annotations	1.0	null
hsa-miR-421	TargetScan Predicted Nonconserved microRNA Targets	1.0	0.843347
NCI-H2023	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.992473
ctnnb1_21914722_ls174t_lof_human_gpl570_gds4386	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	1.0	0.242028
JJN3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.43085
LMSU	CCLE Cell Line Gene CNV Profiles	1.0	1.63962
Bcl11b	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	67.145
mRNA_OTX2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.992473
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.91152
DAN-G	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.29912
BCL6-27268052-CHIP-SEQ-BCELLS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Hmga1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	71.9936
VMRC-LCD	COSMIC Cell Line Gene CNV Profiles	1.0	2.93899
PMC12003903-41531_2025_933_MOESM1_ESM.pdf-11-ENSG00000275111_ZNF2	Rummagene Transcription Factor Associations 2026	1.0	null
PMC9574515-mmc2.xls-THP1_60_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
PMC8791933-41598_2022_4817_MOESM3_ESM.xlsx-DUX4_signature_genes-Unnamed_1_DUX4	Rummagene Transcription Factor Associations 2026	1.0	null
GSE214212_2_v_0_chd6_human	RummaGEO Gene Perturbation Signatures	-1.0	null
Nr2e3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	26.1304
TT	CCLE Cell Line Gene CNV Profiles	1.0	1.68851
GSE202434,GSE202438_2_v_14_talazoparib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
MOR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.993533
hsa-miR-4709-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.7397
GSE139016_3_v_1_disulfiram_human	RummaGEO Drug Perturbation Signatures	1.0	null
GSE239844_6_v_0_crizotinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
HCC1171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14529
IRF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	44.9167
ZNF766	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5796
KATOIII	CCLE Cell Line Gene CNV Profiles	-1.0	-2.07156
GSC2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.7556
ZNF410	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.472
Dlx2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	30.1195
OVMANA	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.10187
NCI-H2347	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.870657
hsa-miR-4293	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.2992
HCC1576	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.992473
Pou5f1::Sox2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	89.112
BNC2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.7615
A-375	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32131
intracellular	GO Cellular Component Annotations 2015	1.0	null
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.853223
DU 145	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.12556
SOX4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.2578
metal ion binding	GO Molecular Function Annotations 2015	1.0	null
Hmx2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	49.5209
KMM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.01448
cellular_component	GO Cellular Component Annotations 2015	1.0	null
Irf1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	103.242
GSE238005_0_v_3_c9orf72_human	RummaGEO Gene Perturbation Signatures	1.0	null
Sox11	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	80.1837
MDN1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.44617
GSE138863_3_v_0_disulfiram_human	RummaGEO Drug Perturbation Signatures	1.0	null
PMC9574515-mmc1.xls-THP1_60_min_GM-CSF-Target_Gene_Symbol_GLI2	Rummagene Transcription Factor Associations 2026	1.0	null
496100451_TCx_no dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.10941
Rfx6	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	25.0457
HCC1195	CCLE Cell Line Gene CNV Profiles	1.0	1.78757
GSE180185_9_v_8_setbp1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
MEF2C	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	111.015
CORL311	CCLE Cell Line Gene CNV Profiles	1.0	1.77671
mRNA_ELF1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
regulation of gene expression	GO Biological Process Annotations 2025	1.0	null
T47D	CCLE Cell Line Gene CNV Profiles	-1.0	-1.35536
mRNA_SFPI1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
GSE74251_2_v_1_decitabine_human	RummaGEO Drug Perturbation Signatures	1.0	null
cell part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
NCIH522	CCLE Cell Line Gene CNV Profiles	1.0	2.53386
mRNA_SOX9_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-3.25411
REST	ENCODE Transcription Factor Targets	1.0	null
LP-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.30866
cell	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
mRNA_ASCL1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
hsa-miR-548k	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.55165
NKX6-1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.2144
ZNF384	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	328.785
brain	GTEx Tissue Gene Expression Profiles	1.0	1.08368
Colon carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.312
mRNA_SMAD7_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
HCC202	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.39688
gata3_21892208_mda_mb_231_gof_human_gpl570_gds4080	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	-1.0	-0.256772
Foxn1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	14.7765
KLF4-19829295-ESCS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
Epididymosome	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.942
Nr1h3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	39.6924
Zinc finger, RING-type	InterPro Predicted Protein Domain Annotations	1.0	null
ZNF680	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.8462
nucleus	LOCATE Predicted Protein Localization Annotations	1.0	null
intracellular organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
NR3C2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.8241
JHH6	CCLE Cell Line Gene CNV Profiles	1.0	1.44297
hsa-miR-3647-5p	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.20993
DMS 454	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.51846
NCIH889	CCLE Cell Line Gene CNV Profiles	1.0	1.37521
Rxra	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	52.05
BHLHE23	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.7567
MKN7	CCLE Cell Line Gene CNV Profiles	-1.0	-1.91441
PMC8791933-41598_2022_4817_MOESM3_ESM.xlsx-DUX4_signature_genes-Unnamed_2_DUX4	Rummagene Transcription Factor Associations 2026	1.0	null
Nr1h2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	14.5394
NCIH2023	CCLE Cell Line Gene CNV Profiles	-1.0	-1.35187
Retinitis pigmentosa	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.024
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.0031
Hoxa11	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	48.5417
Mecom	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	45.1852
NCI-H23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.55124
hsa-miR-623	TargetScan Predicted Nonconserved microRNA Targets	1.0	1.0155
PHOX2B-30127528-KELLY-HUMAN-BRAINNEUROBLASTOMA	ChEA Transcription Factor Targets 2022	1.0	null
Stat2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	386.553
ZNF558	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	153.232
496100342_PCx_no dementia_no TBI_81_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	5.21479
GSE233679_6_v_3_nicotinamide_human	RummaGEO Drug Perturbation Signatures	1.0	null
Foxj2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	69.8498
GSE111247_2_v_1_temozolomide_human	RummaGEO Drug Perturbation Signatures	1.0	null
IRF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	88.3019
POU2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.0778
TCF3/E2A-22897851-JUKARTE6-1-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
NCI-H889	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.32131
intracellular part	LOCATE Predicted Protein Localization Annotations	1.0	null
Zinc finger, B-box	InterPro Predicted Protein Domain Annotations	1.0	null
CAL78	CCLE Cell Line Gene CNV Profiles	1.0	1.49829
GSE195559_2_v_7_notch1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
HCC4011	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.55124
Skeletal Muscle Male	Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles	-1.0	-1.09406
SPRY domain	InterPro Predicted Protein Domain Annotations	1.0	null
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.86957
GSE135244_0_v_1_trdmt1_human	RummaGEO Gene Perturbation Signatures	-1.0	null
LS123	CCLE Cell Line Gene CNV Profiles	1.0	1.51397
WM983B	CCLE Cell Line Gene CNV Profiles	1.0	1.59808
TP63	ChEA Transcription Factor Targets	1.0	null
GSE168797_2_v_0_cannabidiol_human	RummaGEO Drug Perturbation Signatures	1.0	null
Erg	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	40.5898
cell part	LOCATE Predicted Protein Localization Annotations	1.0	null
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-2.3514
SEPTIN7	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.22873
WDR75	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.22282
Hmx3	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	33.1483
PMC7021771-41467_2020_14684_MOESM7_ESM.xlsx-CASZ1_ChIPseq_in_SMS-CTR_MEKi-Gene_Name_CASZ1	Rummagene Transcription Factor Associations 2026	1.0	null
FOSL2_HepG2_hg19_1	ENCODE Transcription Factor Binding Site Profiles	1.0	null
Nobox	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	28.0526
BARX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.5993
496100419_TCx_no dementia_TBI_78_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	14.3249
mRNA_ZFAND3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
LOX-IMVI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.941377
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.09019
MDA-MB-330	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.29912
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.0587
Nkx2-1	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	16.9601
AUTS2-25519132-293T-REX-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null
intracellular	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.03318
Stat4	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	77.6561
BGC823	CCLE Cell Line Gene CNV Profiles	1.0	1.40577
mRNA_CBX8_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
PHOX2A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	40.5344
KYSE-520	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.24661
protein modification by small protein conjugation	GO Biological Process Annotations 2023	1.0	null
Nfe2l2	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	28.9904
NCI-H1734	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.92855
Arid3b	JASPAR Predicted Mouse Transcription Factor Targets 2025	1.0	35.3938
496100633_TCx_no dementia_TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.37428
TP63-22573176-HFKS-HUMAN	ChEA Transcription Factor Targets 2022	1.0	null