association	dataset	threshold value	standardized value
496100537_FWM_no dementia_TBI_87_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07683
nucleus	GO Cellular Component Annotations 2015	1.0	null
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	44.087
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
KMS-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.3574
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
PDCD11	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	1.0	2.36035
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
G121	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
MDN1	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.44617
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
regulation of primary metabolic process	GO Biological Process Annotations 2015	1.0	null
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	88.9034
macromolecule metabolic 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
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
TRPS1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5529
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8265
ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
Foreskin fibroblast cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.476
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	41.2992
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
cellular 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
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	49.1916
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.148
GSE135400_1_v_0_kdm1b_human	RummaGEO Gene Perturbation Signatures	1.0	null
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
cellular process	GO Biological Process Annotations 2015	1.0	null
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	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	-2.07659
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.957
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.0547
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6179
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
HCC4006	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	89.442
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.65384
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
catabolic process	GO Biological Process Annotations 2015	1.0	null
496100616_FWM_no dementia_TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07551
496100303_HIP_no dementia_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07796
496100360_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	-2.07291
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.6525
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
NCI-H2171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
ZNF75A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.6631
NCI-H358	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.2129
TGIF2LX	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.6257
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
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
MOLP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.848
496100641_PCx_no dementia_no TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.18263
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
biological regulation	GO Biological Process Annotations 2015	1.0	null
GSE150134_1_v_0_fluorouracil_human	RummaGEO Drug Perturbation Signatures	-1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
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	-2.07824
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.2719
molecular_function	GO Molecular Function Annotations 2015	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
FOSL1::JUND	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.2491
BACH1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.9163
496100476_TCx_no dementia_TBI_88_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	2.07818
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
SREBF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.156
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
35 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.849
496100432_TCx_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07817
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
ubiquitinyl hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
TGIF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.5484
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
catalytic activity	GO Molecular Function Annotations 2015	1.0	null
prostate	HPA Tissue Protein Expression Profiles	1.0	1.32926
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.8282
protein metabolic process	GO Biological Process Annotations 2015	1.0	null
GSE122425_1_v_0_nsun2_human	RummaGEO Gene Perturbation Signatures	-1.0	null
GSE150134_1_v_0_scn5a_human	RummaGEO Gene Perturbation Signatures	-1.0	null
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
496100634_HIP_no dementia_TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07845
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.515
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036
fallopian tube	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
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
GTL-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
PORCN	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.02534
WIDR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
496100529_HIP_no dementia_no TBI_89_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07365
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
GSE193351_1_v_0_ruxolitinib_human	RummaGEO Drug Perturbation Signatures	1.0	null
CREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.6179
Skin fibroblast cell line	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.383
endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
HS729	CCLE Cell Line Gene CNV Profiles	1.0	1.62118
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.3781
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.599
JHH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
496100445_HIP_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07752
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
496100430_PCx_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07794
496100352_FWM_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07201
496100614_PCx_no dementia_TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07844
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
nucleus	GO Cellular Component Annotations 2025	1.0	null
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
FOSL2::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.95
496100277_FWM_no dementia_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07538
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.8567
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
496100511_TCx_no dementia_no TBI_89_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07727
ubiquitin-like protein-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79416
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
SNU-C1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
THOC2	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.11415
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
TGIF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	34.4157
HS695T	CCLE Cell Line Gene CNV Profiles	1.0	1.73114
cell part	GO Cellular Component Annotations 2015	1.0	null
AMO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.122
GATA6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.7381
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	96.2452
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.0034
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
organic substance metabolic process	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
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
Ub-specific processing proteases	Reactome Pathways 2024	1.0	null
clathrin-coated pit	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.106
macromolecule modification	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
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
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	-2.07827
cervix uteri	GTEx Tissue Gene Expression Profiles	1.0	0.886838
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
HUH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
regulation of protein catabolic process	GO Biological Process Annotations 2015	1.0	null
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4245
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
FOS	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.2154
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
pituitary	GTEx Tissue Gene Expression Profiles	1.0	1.26014
PMC10335698-pone.0285806.s007.xlsx-DMKN-shRNA_KD_Vs_ShSrc-Unnamed_5_AR	Rummagene Transcription Factor Associations 2026	1.0	null
nucleus	GO Cellular Component Annotations 2023	1.0	null
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.4809
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.5965
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
ZFP42	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.0896
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
cellular protein modification process	GO Biological Process Annotations 2015	1.0	null
496100633_TCx_no dementia_TBI_84_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07845
HCC1500	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	1.102
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
protein modification 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
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
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
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8105
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
PKNOX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.5744
JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.6638
biological_process	GO Biological Process Annotations 2015	1.0	null
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
FOSL1::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.285
496100523_HIP_possible Alzheimer's disease_no TBI_90-94_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07657
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
modification-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
SKMEL1	CCLE Cell Line Gene CNV Profiles	1.0	3.27631
496100388_HIP_probable Alzheimer's disease_no TBI_87_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07819
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.6208
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
regulation of metabolic process	GO Biological Process Annotations 2015	1.0	null
Post-translational protein modification	Reactome Pathways 2024	1.0	null
496100535_FWM_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07726
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	218.636
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
REH	CCLE Cell Line Gene CNV Profiles	1.0	1.41854
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
MS751	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
peptidase activity, acting on l-amino acid peptides	GO Molecular Function Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.1172
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
COLO 699	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
EBF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	47.8758
Metabolism of proteins	Reactome Pathways 2024	1.0	null
RARA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	58.1165
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
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
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
cellular macromolecule 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
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.6404
organic substance 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
Deubiquitination	Reactome Pathways 2024	1.0	null
GATA4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.0127
regulation of cellular protein catabolic 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
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.148
HS 695T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.08795
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
metabolic process	GO Biological Process Annotations 2015	1.0	null
GSE187006_3_v_2_valproic acid_human	RummaGEO Drug Perturbation Signatures	1.0	null
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	38.1006
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
488395315_TCx_no dementia_no TBI_90-94_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07569
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
cellular_component	GO Cellular Component Annotations 2015	1.0	null
NCI-H2461	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.02444
NCI-H1581	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.938616
GSE135400_2_v_0_kdm1b_human	RummaGEO Gene Perturbation Signatures	1.0	null
proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
496100532_FWM_no dementia_no TBI_89_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	-1.0	-2.07543
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
protein modification by small protein conjugation or removal	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 proteolysis	GO Biological Process Annotations 2015	1.0	null
KLF9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	144.878
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
cellular macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	91.5095
organelle	GO Cellular Component Annotations 2015	1.0	null
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
KELLY	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79249
macromolecule 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
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
Ubiquitin specific protease domain	InterPro Predicted Protein Domain Annotations	1.0	null
HEP-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
SCC-25	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.7034
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
TGIF2LY	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.7506
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
PSMG3	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	-1.0	-2.2836
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8627
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
OPM-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
NR2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9564