association	dataset	threshold value	standardized value
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
SCC-25	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H1568	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	34.9103
496100545_HIP_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	2.20191
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
GATA6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.7734
PMC6961462-NIHMS1544104-supplement-Sup_Tab.xlsx-Sup_Table_3_a-Supplementary_Table_3_Genes_Regulated_by_A_MYB_in_Humans_and_Macaques_Bold_genes_with_reduced_expression_in_Group_3_MYB	Rummagene Transcription Factor Associations 2026	1.0	null
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	71.6482
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79249
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5535
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
NKX2-2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4076
proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.2719
496100670_TCx_probable Alzheimer's disease_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.37242
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4609
Post-translational protein modification	Reactome Pathways 2024	1.0	null
cellular macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.8783
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.6087
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
496100542_PCx_no dementia_no TBI_82_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.38739
JHH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
PMC8709578-elife-69843-supp2.xlsx-HSF1_KO_2_Ctr-Gene_Name_HSF1	Rummagene Transcription Factor Associations 2026	1.0	null
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.271
protein metabolic process	GO Biological Process Annotations 2015	1.0	null
HCC70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.828501
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
WIDR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.2708
proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
catalytic activity	GO Molecular Function Annotations 2015	1.0	null
endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
496100447_HIP_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.26268
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
nucleus	GO Cellular Component 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
macromolecule catabolic 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
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.4883
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.1503
regulation of cellular catabolic process	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	2.9552
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.0187
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	3.57828
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5763
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
Skin fibroblast cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.825
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
KLF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	116.515
496100416_FWM_dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.19064
TCF4-32651957-PLC/PRF/5-HUMAN-LIVER-HEPTOMA	ChEA Transcription Factor Targets 2022	1.0	null
Ubiquitin specific protease domain	InterPro Predicted Protein Domain Annotations	1.0	null
PBX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9613
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
NIH:OVCAR-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
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	2.31597
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
PK-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54773
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
organic substance metabolic process	GO Biological Process Annotations 2015	1.0	null
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
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
Microtubule organizing center attachment site	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.225
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.047
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
496100626_FWM_no dementia_TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.01602
496100378_TCx_probable Alzheimer's disease_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.20129
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
Foreskin fibroblast cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.918
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
PMC4387713-supp_gad.255984.114_Table_S5.xlsx-S5E-Down_H3K27me3_DPY30_KD-Unnamed_12_AR	Rummagene Transcription Factor Associations 2026	1.0	null
regulation of metabolic process	GO Biological Process Annotations 2015	1.0	null
496100400_PCx_dementia_TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.02364
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
biological regulation	GO Biological Process Annotations 2015	1.0	null
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	62.9735
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
MDA-MB-330	COSMIC Cell Line Gene CNV Profiles	-1.0	-5.12655
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
496100571_FWM_dementia_TBI_81_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.24383
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
SREBF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.156
regulation of protein catabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
PAX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.5116
496100589_PCx_dementia_TBI_81_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.03741
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	2.87164
cellular process	GO Biological Process Annotations 2015	1.0	null
PMC8709578-elife-69843-supp2.xlsx-HSF1_KO_2_Ctr-Nearest_Ensembl_HSF1	Rummagene Transcription Factor Associations 2026	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.4861
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
SKMEL1	CCLE Cell Line Gene CNV Profiles	1.0	3.27631
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
HCC4006	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
NCI-H1435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.0942
TRPS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.522
cellular macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
NCI-H446	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9725
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
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	2.62061
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.46108
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
GATA4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.6933
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79416
proteolysis	GO Biological Process Annotations 2015	1.0	null
Metabolism of proteins	Reactome Pathways 2024	1.0	null
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.4924
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
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	3.53422
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	2.7284
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
ELF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5949
cellular_component	GO Cellular Component Annotations 2015	1.0	null
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
496100424_FWM_probable Alzheimer's disease_TBI_88_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.35019
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
ubiquitinyl hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.271
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.1146
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
organic substance catabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
molecular_function	GO Molecular Function Annotations 2015	1.0	null
STAT3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.2107
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	2.35
intracellular part	GO Cellular Component Annotations 2015	1.0	null
HCC1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.39131
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
MS751	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
496100525_TCx_probable Alzheimer's disease_no TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.65813
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	61.5374
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
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
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1006
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
496100486_PCx_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.41431
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
Deubiquitination	Reactome Pathways 2024	1.0	null
496100332_HIP_possible Alzheimer's disease_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.21478
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
PK-45P	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.28598
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4929
496100576_HIP_dementia_TBI_81_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.3996
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	2.69407
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
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
NCI-H1581	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.938616
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
496100534_FWM_probable Alzheimer's disease_no TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.49563
HOXA5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.9097
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.971
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
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
SNU-C1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
SIX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.5454
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
macromolecule modification	GO Biological Process Annotations 2015	1.0	null
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
nucleus	GO Cellular Component Annotations 2023	1.0	null
cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
NCI-H2461	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.02444
protein modification process	GO Biological Process Annotations 2015	1.0	null
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.8303
SNU-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
HS695T	CCLE Cell Line Gene CNV Profiles	1.0	1.73114
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
FOSL1::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.958
NCI-H358	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
metabolic 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
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.1688
cellular protein modification 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
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
496100569_TCx_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	2.77782
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
nucleus	GO Cellular Component Annotations 2015	1.0	null
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
496100295_TCx_possible Alzheimer's disease_TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.26326
regulation of cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
organelle	GO Cellular Component Annotations 2015	1.0	null
496100425_TCx_no dementia_TBI_95-99_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.53336
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
AMO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.1519
HS729	CCLE Cell Line Gene CNV Profiles	1.0	1.62118
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	42.5951
fallopian tube	HPA Tissue Protein Expression Profiles	1.0	1.32926
REH	CCLE Cell Line Gene CNV Profiles	1.0	1.41854
catabolic process	GO Biological Process Annotations 2015	1.0	null
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
COLO 699	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
NR2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9564
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
HCC1576	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
496100627_TCx_no dementia_TBI_86_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.75203
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
KMS-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
CA SKI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14515
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
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
G121	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
BJ cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.069
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
496100466_PCx_probable Alzheimer's disease_no TBI_89_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	3.35737
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.634
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
496100552_PCx_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	3.01164
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
regulation of proteolysis	GO Biological Process Annotations 2015	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
496100433_HIP_probable Alzheimer's disease_TBI_88_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.18568
HCC1493	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42358
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.8945
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
modification-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
FOSL2::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.599
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
PMC12719073-mmc1.pdf-14-MYSM1_MYSM1	Rummagene Transcription Factor Associations 2026	1.0	null
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
496100490_HIP_no dementia_no TBI_86_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.08999
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.08795
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.245
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	2.83423
PMC10149505-41392_2023_1393_MOESM2_ESM.xlsx-CPCMR-Hugo_Symbol_MEIS2	Rummagene Transcription Factor Associations 2026	1.0	null
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
regulation of primary metabolic process	GO Biological Process Annotations 2015	1.0	null
cell part	GO Cellular Component Annotations 2015	1.0	null
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	63.484
HUH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.3978
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
ubiquitin-like protein-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	138.455