association	dataset	threshold value	standardized value
Ub-specific processing proteases	Reactome Pathways 2024	1.0	null
proteolysis involved in cellular 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
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.46108
fallopian tube	HPA Tissue Protein Expression Profiles	1.0	1.32926
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	71.6499
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.3978
HCC70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.828501
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
NKX2-2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4076
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H358	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
nucleus	GO Cellular Component Annotations 2023	1.0	null
regulation of protein catabolic process	GO Biological Process Annotations 2015	1.0	null
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.0942
organic substance catabolic process	GO Biological Process Annotations 2015	1.0	null
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1006
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
OPM-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.4924
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
cellular macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
HCC1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.39131
STAT3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.2107
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.6087
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
nucleus	GO Cellular Component Annotations 2025	1.0	null
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
pre-replicative complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.825
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	84.3232
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_1_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.0622
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
organic substance metabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
CA SKI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14515
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
ubiquitinyl hydrolase 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
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.1146
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.634
GATA6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.7734
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
protein metabolic process	GO Biological Process Annotations 2015	1.0	null
macromolecule modification	GO Biological Process Annotations 2015	1.0	null
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
cell part	GO Cellular Component Annotations 2015	1.0	null
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
NCI-H446	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	42.5951
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4609
protein modification by small protein conjugation or removal	GO Biological Process Annotations 2015	1.0	null
ELF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5949
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
Post-translational protein modification	Reactome Pathways 2024	1.0	null
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
ubiquitin-like protein-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4929
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
PK-45P	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.28598
regulation of primary metabolic 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
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.662
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.8303
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
Microtubule organizing center attachment site	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.234
nucleus	GO Cellular Component Annotations 2015	1.0	null
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
PBX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9613
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	34.9103
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
HCC4006	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H1581	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.938616
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
KLF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	124.216
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	18.3324
regulation of cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
TCF4-32651957-PLC/PRF/5-HUMAN-LIVER-HEPTOMA	ChEA Transcription Factor Targets 2022	1.0	null
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
PK-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54773
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
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
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
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
HEP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.0187
metabolic process	GO Biological Process Annotations 2015	1.0	null
molecular_function	GO Molecular Function Annotations 2015	1.0	null
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
HS729	CCLE Cell Line Gene CNV Profiles	1.0	1.62118
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5763
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
cellular macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
ubiquitin-dependent protein catabolic 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
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.98
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.2708
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.281
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79416
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
MS751	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
organelle	GO Cellular Component Annotations 2015	1.0	null
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.1519
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.146
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
intracellular membrane-bounded organelle	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
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.281
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
Metabolism of proteins	Reactome Pathways 2024	1.0	null
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
protein modification process	GO Biological Process Annotations 2015	1.0	null
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
HCC1493	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42358
SNU-C1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	159.364
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.4883
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.254
SIX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.5454
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
regulation of metabolic process	GO Biological Process Annotations 2015	1.0	null
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.65384
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
NCI-H2171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	74.9286
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
SKMEL1	CCLE Cell Line Gene CNV Profiles	1.0	3.27631
HUH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
NR2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9564
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
PMC10335698-pone.0285806.s007.xlsx-DMKN-shRNA_KD_Vs_ShSrc-Unnamed_7_AR	Rummagene Transcription Factor Associations 2026	1.0	null
modification-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
MDA-MB-330	COSMIC Cell Line Gene CNV Profiles	-1.0	-5.12655
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
496100418_TCx_no dementia_TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.33071
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.3393
WIDR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
HS695T	CCLE Cell Line Gene CNV Profiles	1.0	1.73114
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
GATA4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.6933
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
NCI-H1568	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
cellular protein modification process	GO Biological Process Annotations 2015	1.0	null
NCI-H2461	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.02444
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.8335
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5535
regulation of proteolysis	GO Biological Process Annotations 2015	1.0	null
cellular_component	GO Cellular Component Annotations 2015	1.0	null
PAX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.5116
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
COLO 699	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
catalytic 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
prostate	HPA Tissue Protein Expression Profiles	1.0	1.32926
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
TRPS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.522
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
cellular process	GO Biological Process Annotations 2015	1.0	null
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9725
peptidase activity, acting on l-amino acid peptides	GO Molecular Function Annotations 2015	1.0	null
GTL-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
proteolysis	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
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79249
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.1503
ZNF75A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.6631
cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
catabolic process	GO Biological Process Annotations 2015	1.0	null
biological regulation	GO Biological Process Annotations 2015	1.0	null
deubiquitinase activity	GO Molecular Function Annotations 2023	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
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
REH	CCLE Cell Line Gene CNV Profiles	1.0	1.41854
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
Deubiquitination	Reactome Pathways 2024	1.0	null
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
SNU-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
G121	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
intracellular part	GO Cellular Component Annotations 2015	1.0	null
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.1688
PMC7397849-supp_gad.338681.120_Supplemental_Table_S3.xlsx-S3M_Peaks_YAP1MAMLD1_TEAD4-Unnamed_11_TEAD4	Rummagene Transcription Factor Associations 2026	1.0	null
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
biological_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
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	75.8673
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036