association	dataset	threshold value	standardized value
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
Amylin receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.956
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
OPM-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
peptidase activity, acting on l-amino acid peptides	GO Molecular Function Annotations 2015	1.0	null
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
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
HUH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
NCI-H1581	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.938616
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.0622
biological_process	GO Biological Process Annotations 2015	1.0	null
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.144
NCI-H358	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
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	17.7438
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
vagina	GTEx Tissue Gene Expression Profiles	1.0	0.896764
macromolecule modification	GO Biological Process Annotations 2015	1.0	null
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
catabolic process	GO Biological Process Annotations 2015	1.0	null
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.634
nucleus	GO Cellular Component Annotations 2023	1.0	null
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.8335
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
cellular macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.3978
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
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
KLF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	124.705
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4929
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
SNU-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
GATA2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6565
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
cell part	GO Cellular Component Annotations 2015	1.0	null
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
HCC70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.828501
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4609
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	71.6499
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
regulation of cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.65384
JHH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.4883
molecular_function	GO Molecular Function Annotations 2015	1.0	null
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.08795
Post-translational protein modification	Reactome Pathways 2024	1.0	null
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
GTL-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
catalytic activity	GO Molecular Function Annotations 2015	1.0	null
regulation of proteolysis	GO Biological Process Annotations 2015	1.0	null
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
cellular_component	GO Cellular Component Annotations 2015	1.0	null
NIH:OVCAR-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
HCC4006	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.957
TRPS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.1062
regulation of metabolic process	GO Biological Process Annotations 2015	1.0	null
proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
NCI-H446	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
nucleus	GO Cellular Component Annotations 2025	1.0	null
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.17
nucleus	GO Cellular Component Annotations 2015	1.0	null
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
cellular macromolecule metabolic 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
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
HEP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
HCC1576	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
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
NCI-H1435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
PBX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9613
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
ELF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5949
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
regulation of protein catabolic 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
GATA4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.3708
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
HCC1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.39131
PK-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54773
thyroid	GTEx Tissue Gene Expression Profiles	1.0	0.862748
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	39.1146
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.6087
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
TK	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
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
GATA6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.4165
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_1_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	42.5951
Metabolism of proteins	Reactome Pathways 2024	1.0	null
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9725
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.0187
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
biological regulation	GO Biological Process Annotations 2015	1.0	null
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
Amylin receptor complex 1	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.045
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	75.8673
regulation of cellular 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
SIX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	27.3019
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
496100409_FWM_no dementia_TBI_85_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	4.963
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 cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
prostate	HPA Tissue Protein Expression Profiles	1.0	1.32926
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
organic substance metabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
Deubiquitination	Reactome Pathways 2024	1.0	null
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.2708
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
SKMEL1	CCLE Cell Line Gene CNV Profiles	1.0	3.27631
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.8945
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
fallopian tube	HPA Tissue Protein Expression Profiles	1.0	1.32926
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5535
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
cellular process	GO Biological Process Annotations 2015	1.0	null
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_5_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5763
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.1519
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.1503
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
PAX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.5116
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
SCC-25	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
proteasomal protein catabolic 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
Calcitonin family receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.768
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_9_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
KMS-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	34.9103
MS751	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
NCI-H2461	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.02444
organic substance catabolic process	GO Biological Process Annotations 2015	1.0	null
AMO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
proteolysis	GO Biological Process Annotations 2015	1.0	null
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.1688
NKX2-2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4076
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.46108
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.4924
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
496100407_FWM_probable Alzheimer's disease_no TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	5.03915
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
cellular protein modification process	GO Biological Process Annotations 2015	1.0	null
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
protein metabolic process	GO Biological Process Annotations 2015	1.0	null
blood vessel	GTEx Tissue Gene Expression Profiles	-1.0	-0.836968
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
protein modification by small protein conjugation or removal	GO Biological Process Annotations 2015	1.0	null
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	14.8303
ubiquitinyl hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.17
endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
CA SKI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14515
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
organelle	GO Cellular Component Annotations 2015	1.0	null
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
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
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
STAT3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.2107
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	84.3232
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
macromolecule catabolic 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
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	177.364
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
intracellular part	GO Cellular Component Annotations 2015	1.0	null
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1006
NCI-H2171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
PK-45P	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.28598
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
TCF4-32651957-PLC/PRF/5-HUMAN-LIVER-HEPTOMA	ChEA Transcription Factor Targets 2022	1.0	null
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.662
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
brain	GTEx Tissue Gene Expression Profiles	1.0	2.18987
ubiquitin-like protein-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.0942
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
pituitary	GTEx Tissue Gene Expression Profiles	1.0	1.04044
HOXA5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.9097
Microtubule organizing center attachment site	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.124
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	2.69887
regulation of primary metabolic 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
MDA-MB-330	COSMIC Cell Line Gene CNV Profiles	-1.0	-5.12655
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79249
Ub-specific processing proteases	Reactome Pathways 2024	1.0	null
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
esophagus	GTEx Tissue Gene Expression Profiles	-1.0	-1.4446
metabolic process	GO Biological Process Annotations 2015	1.0	null
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	68.2322
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.869
modification-dependent protein 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
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
protein modification process	GO Biological Process Annotations 2015	1.0	null