association	dataset	threshold value	standardized value
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
SNU-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4609
496100627_TCx_no dementia_TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	4.91248
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.46108
HCC4006	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
G121	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
peptidase activity, acting on l-amino acid peptides	GO Molecular Function Annotations 2015	1.0	null
regulation of cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H1435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
HEP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
regulation of cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1006
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	71.6499
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
Connective tissue	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
PAX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.5116
496100542_PCx_no dementia_no TBI_82_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.24858
ubiquitinyl hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
HS695T	CCLE Cell Line Gene CNV Profiles	1.0	1.73114
REH	CCLE Cell Line Gene CNV Profiles	1.0	1.41854
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
organic substance catabolic process	GO Biological Process Annotations 2015	1.0	null
organelle	GO Cellular Component Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.328
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
Urinary system	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
496100403_TCx_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.3654
STAT3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.2107
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
regulation of primary metabolic process	GO Biological Process Annotations 2015	1.0	null
Immune system	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
NCI-H1568	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.3978
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.0187
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
cellular catabolic 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
SIX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.5454
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
496100467_FWM_probable Alzheimer's disease_no TBI_89_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.24167
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
PK-45P	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.28598
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
Large intestine	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5535
protein modification process	GO Biological Process Annotations 2015	1.0	null
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
PK-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54773
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.16
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79249
cell part	GO Cellular Component Annotations 2015	1.0	null
NKX2-2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4076
MS751	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
GTL-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
HUH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
496100644_HIP_probable Alzheimer's disease_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.7215
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
nucleus	GO Cellular Component Annotations 2025	1.0	null
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
nucleus	GO Cellular Component Annotations 2015	1.0	null
endopeptidase activity	GO Molecular Function Annotations 2023	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	2.89924
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
Post-translational protein modification	Reactome Pathways 2024	1.0	null
Uterus	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
cellular_component	GO Cellular Component Annotations 2015	1.0	null
Stomach	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_1_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
Uterine cervix	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	177.364
nucleus	GO Cellular Component Annotations 2023	1.0	null
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.6087
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
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	3.34511
496100547_HIP_no dementia_no TBI_82_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.42805
PMC12719073-mmc1.pdf-14-MYSM1_MYSM1	Rummagene Transcription Factor Associations 2026	1.0	null
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
NIH:OVCAR-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
Prostate gland	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9725
496100400_PCx_dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.83593
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
molecular_function	GO Molecular Function Annotations 2015	1.0	null
cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79416
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H2171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.662
NCI-H358	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
Bladder	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.1503
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.6208
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
proteolysis	GO Biological Process Annotations 2015	1.0	null
Colorectum	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
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	4.708
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
ELF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5949
496100435_TCx_probable Alzheimer's disease_TBI_88_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.76338
Gastrointestinal tract	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H446	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
ZNF75A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.6631
Lymphoid tissue	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
SNU-C1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
JHH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
Tonsil	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
biological_process	GO Biological Process Annotations 2015	1.0	null
protein modification by small protein conjugation or removal	GO Biological Process Annotations 2015	1.0	null
WIDR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
Oviduct	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	68.2322
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
496100475_TCx_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.41996
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
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	3.01415
TRPS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.522
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
496100392_HIP_dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.56282
496100447_HIP_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.74358
496100623_PCx_no dementia_TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	5.23692
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.027
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
Epididymis	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
Kawasaki disease	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.031
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5763
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.0622
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.8303
Internal male genital organ	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
cellular process	GO Biological Process Annotations 2015	1.0	null
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
Viscus	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.1519
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.1146
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.301
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
SCC-25	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
Rectum	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
regulation of protein catabolic process	GO Biological Process Annotations 2015	1.0	null
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
496100484_FWM_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.21993
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
cellular macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
NCI-H1581	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.938616
modification-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
Colon	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
KLF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	124.705
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
Male reproductive gland	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
metabolic process	GO Biological Process Annotations 2015	1.0	null
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.4883
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.0942
Urinary tract	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
intracellular part	GO Cellular Component Annotations 2015	1.0	null
496100370_PCx_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.13172
biological regulation	GO Biological Process Annotations 2015	1.0	null
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.2708
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.1688
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
Male reproductive system	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.634
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
protein metabolic process	GO Biological Process Annotations 2015	1.0	null
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	42.6026
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.328
Microtubule organizing center attachment site	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.281
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
COLO 699	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
organic substance metabolic process	GO Biological Process Annotations 2015	1.0	null
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
prostate	HPA Tissue Protein Expression Profiles	1.0	1.32926
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.65384
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
cellular protein modification process	GO Biological Process Annotations 2015	1.0	null
Urinary bladder	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
fallopian tube	HPA Tissue Protein Expression Profiles	1.0	1.32926
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
HCC1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.39131
GATA6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.7734
ubiquitin-like protein-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
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
Metabolism of proteins	Reactome Pathways 2024	1.0	null
Alimentary canal	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
HS729	CCLE Cell Line Gene CNV Profiles	1.0	1.62118
deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
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	3.78399
Gall bladder	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
496100490_HIP_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.70415
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	75.8673
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036
PBX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9613
cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.08795
regulation of proteolysis	GO Biological Process Annotations 2015	1.0	null
HCC70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.828501
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
OPM-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
Ub-specific processing proteases	Reactome Pathways 2024	1.0	null
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
Intestine	TISSUES Experimental Tissue Protein Expression Evidence Scores 2025	1.0	1.091
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
Deubiquitination	Reactome Pathways 2024	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
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.3393
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
macromolecule modification	GO Biological Process Annotations 2015	1.0	null
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.8335
NCI-H2461	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.02444
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_9_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
AMO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
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	8.30479
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
496100421_PCx_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.55837
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
regulation of metabolic 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
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
NR2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9564
CA SKI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14515
GATA4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.6933
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	34.9103
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
catalytic activity	GO Molecular Function Annotations 2015	1.0	null
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	84.3232
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4929
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.4924
SKMEL1	CCLE Cell Line Gene CNV Profiles	1.0	3.27631
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
496100379_TCx_probable Alzheimer's disease_no TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.59546
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_5_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
cellular macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null