association	dataset	threshold value	standardized value
AMO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
cellular_component	GO Cellular Component Annotations 2015	1.0	null
ZFP42	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.6176
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
Protein phosphatase 4 complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.084
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_1_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
OPM-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
GSE143994_2_v_1_ythdf1_human	RummaGEO Gene Perturbation Signatures	1.0	null
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79416
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
GSE193351_1_v_0_ruxolitinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
catalytic activity	GO Molecular Function Annotations 2015	1.0	null
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.8303
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.6404
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
FOSL1::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.958
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
metabolic process	GO Biological Process Annotations 2015	1.0	null
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
HEP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
PK-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54773
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	-2.44308
HS695T	CCLE Cell Line Gene CNV Profiles	1.0	1.73114
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
protein modification process	GO Biological Process Annotations 2015	1.0	null
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
496100541_FWM_possible Alzheimer's disease_no TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44516
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.0187
WIDR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
PK-45P	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.28598
NR2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9564
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
496100292_PCx_no dementia_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.4452
PMC10709143-41556_2023_1271_MOESM9_ESM.xls-Up_in_PAX7-Target_name_PAX7	Rummagene Transcription Factor Associations 2026	1.0	null
Oc cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.074
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
ubiquitinyl hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
ATF6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.2986
496100287_TCx_no dementia_TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44457
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
PBX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9613
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.062
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
heart	GTEx Tissue Gene Expression Profiles	-1.0	-1.28744
496100492_TCx_probable Alzheimer's disease_no TBI_89_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44495
nucleus	GO Cellular Component Annotations 2015	1.0	null
liver	GTEx Tissue Gene Expression Profiles	-1.0	-1.43361
HS729	CCLE Cell Line Gene CNV Profiles	1.0	1.62118
HCC1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.39131
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.7034
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
SMAD3-30307970-HCASMC-HUMAN-CORONARYARTERY	ChEA Transcription Factor Targets 2022	1.0	null
Golgi cis cisterna	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.505
Microtubule organizing center attachment site	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.042
496100508_PCx_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	-2.4448
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
prostate	HPA Tissue Protein Expression Profiles	1.0	1.32926
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
496100564_TCx_no dementia_no TBI_82_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44425
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
Mitochondrial respiratory chain complex I	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.776
ubiquitin-like protein-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.9062
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
protein modification by small protein conjugation or removal	GO Biological Process Annotations 2015	1.0	null
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
496100278_FWM_no dementia_TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.1304
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
peptidase activity, acting on l-amino acid peptides	GO Molecular Function Annotations 2015	1.0	null
PMC7397849-supp_gad.338681.120_Supplemental_Table_S3.xlsx-S3M_Peaks_YAP1MAMLD1_TEAD4-Unnamed_14_TEAD4	Rummagene Transcription Factor Associations 2026	1.0	null
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
catabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of protein catabolic process	GO Biological Process Annotations 2015	1.0	null
JHH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
Golgi cisterna membrane	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.649
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
496100434_HIP_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44462
PMC8684775-CTM2-11-e640-s002.xlsx-Sheet1-Table_S3_MAF_file_of_the_CCS_samples_MAF	Rummagene Transcription Factor Associations 2026	1.0	null
cell part	GO Cellular Component Annotations 2015	1.0	null
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
496100554_FWM_no dementia_no TBI_78_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.28208
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
NCI-H358	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
496100505_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	-2.44474
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
496100475_TCx_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.4448
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	84.3232
496100423_PCx_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.322
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.089
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.4861
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
macromolecule modification	GO Biological Process Annotations 2015	1.0	null
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
496100392_HIP_dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44356
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
cellular process	GO Biological Process Annotations 2015	1.0	null
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.6087
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
GSX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	12.7031
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.46108
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
cellular macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
PMC12000322-41419_2025_7601_MOESM9_ESM.xlsx-H3122-AR_somatic_filtered_PASS-Unnamed_47_AR	Rummagene Transcription Factor Associations 2026	1.0	null
496100566_FWM_no dementia_no TBI_82_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44459
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.79
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
Ovary adenocarcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.048
a2780cis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.691
496100497_FWM_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44227
macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6179
LNCaP clone FGC	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.37
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
intracellular part	GO Cellular Component Annotations 2015	1.0	null
NCI-H2171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.8783
organic substance catabolic process	GO Biological Process Annotations 2015	1.0	null
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
biological_process	GO Biological Process Annotations 2015	1.0	null
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
KMS-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
Golgi lumen	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.95
cis-Golgi network	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.135
496100417_HIP_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44426
PMC12000322-41419_2025_7601_MOESM9_ESM.xlsx-H3122-AR_somatic_filtered_PASS-Unnamed_60_AR	Rummagene Transcription Factor Associations 2026	1.0	null
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.2147
proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
496100523_HIP_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	-2.44394
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
Plant cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.068
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5535
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
brain	GTEx Tissue Gene Expression Profiles	1.0	1.0796
SNU-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
SREBF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.156
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
Metabolism of proteins	Reactome Pathways 2024	1.0	null
GSE149901_2_v_1_anlotinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.3781
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
HCC1493	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42358
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.65384
biological regulation	GO Biological Process Annotations 2015	1.0	null
molecular_function	GO Molecular Function Annotations 2015	1.0	null
CA SKI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14515
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
regulation of cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.4883
pituitary	GTEx Tissue Gene Expression Profiles	1.0	1.58475
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
496100484_FWM_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.31429
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
cellular protein modification process	GO Biological Process Annotations 2015	1.0	null
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.6208
496100288_HIP_no dementia_TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44489
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
SCC-25	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
496100665_PCx_probable Alzheimer's disease_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44508
TCF4-32651957-PLC/PRF/5-HUMAN-LIVER-HEPTOMA	ChEA Transcription Factor Targets 2022	1.0	null
fallopian tube	HPA Tissue Protein Expression Profiles	1.0	1.32926
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_5_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
HCC1576	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
Golgi cisterna	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.102
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_9_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.3978
modification-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1006
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
Endometrioid ovary carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.771
A-2780 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.132
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.8567
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.1146
SNU-C1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.788
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
NIH:OVCAR-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
nucleus	GO Cellular Component Annotations 2023	1.0	null
G121	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
496100658_FWM_probable Alzheimer's disease_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44526
PMC11749115-loae020_suppl_Supplementary_Table_S2.xlsx-CHOP-high-gene_DDIT3	Rummagene Transcription Factor Associations 2026	1.0	null
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
Foreskin fibroblast cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.661
Ubiquitin specific protease domain	InterPro Predicted Protein Domain Annotations	1.0	null
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79249
HUH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	68.2322
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
Ub-specific processing proteases	Reactome Pathways 2024	1.0	null
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	71.6499
PMC7397849-supp_gad.338681.120_Supplemental_Table_S3.xlsx-S3M_Peaks_YAP1MAMLD1_TEAD4-Unnamed_11_TEAD4	Rummagene Transcription Factor Associations 2026	1.0	null
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
proteolysis	GO Biological Process Annotations 2015	1.0	null
496100512_PCx_probable Alzheimer's disease_no TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44497
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
PMC12719073-mmc1.pdf-14-MYSM1_MYSM1	Rummagene Transcription Factor Associations 2026	1.0	null
NCI-H446	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
35 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.682
endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
protein metabolic process	GO Biological Process Annotations 2015	1.0	null
organelle	GO Cellular Component Annotations 2015	1.0	null
GSE193351_1_v_3_ruxolitinib_human	RummaGEO Drug Perturbation Signatures	-1.0	null
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
MS751	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.1787
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
HCC4006	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
Deubiquitination	Reactome Pathways 2024	1.0	null
COLO 699	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	75.8673
496100626_FWM_no dementia_TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.00256
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5763
GSE245270_2_v_0_isoproterenol_human	RummaGEO Drug Perturbation Signatures	1.0	null
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
cellular macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
GTL-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
496100542_PCx_no dementia_no TBI_82_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.38315
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
496100297_FWM_possible Alzheimer's disease_TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44519
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
HCC70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.828501
496100527_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	-2.44195
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8627
NCI-H2461	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.02444
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.089
organic substance metabolic process	GO Biological Process Annotations 2015	1.0	null
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
nucleus	GO Cellular Component Annotations 2025	1.0	null
PAX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.7674
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.2719
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
PMC12081856-41420_2025_2522_MOESM6_ESM.xlsx-Sheet_1-Table_S4_Complete_Gene_List_of_the_MEblack_Gene_Module_and_the_DUB_Family_ZUP1	Rummagene Transcription Factor Associations 2026	1.0	null
regulation of proteolysis	GO Biological Process Annotations 2015	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
FOSL2::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.599
REH	CCLE Cell Line Gene CNV Profiles	1.0	1.41854
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
HOXA5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.9097
KLF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	124.705
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.08795
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
NCI-H1568	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	177.364
496100303_HIP_no dementia_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44495
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.8945
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036
496100532_FWM_no dementia_no TBI_89_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44311
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
PMC12000322-41419_2025_7601_MOESM9_ESM.xlsx-H3122-AR_somatic_filtered_PASS-version_2_4_AR	Rummagene Transcription Factor Associations 2026	1.0	null
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
496100431_FWM_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44427
496100291_TCx_no dementia_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44517
regulation of primary metabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
VAX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	12.9499
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
regulation of cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
496100339_HIP_no dementia_TBI_79_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.36484
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
496100368_PCx_probable Alzheimer's disease_no TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44024
MDA-MB-330	COSMIC Cell Line Gene CNV Profiles	-1.0	-5.12655
496100503_HIP_probable Alzheimer's disease_no TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.44487
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
NCI-H1581	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.938616
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
NCI-H1435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
regulation of metabolic process	GO Biological Process Annotations 2015	1.0	null
Post-translational protein modification	Reactome Pathways 2024	1.0	null
SKMEL1	CCLE Cell Line Gene CNV Profiles	1.0	3.27631