association	dataset	threshold value	standardized value
KLF11	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	91.8998
PROX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.2719
SCC-25	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
gallbladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
TMD8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.70088
NCIH441	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.0665
REC1	CCLE Cell Line Gene CNV Profiles	1.0	1.72767
HT	CCLE Cell Line Gene CNV Profiles	-1.0	-1.78493
MDA-MB-175-VII	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54844
mRNA_SOX9_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
SNU601	CCLE Cell Line Gene CNV Profiles	-1.0	-2.26056
Super elongation complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.882
NCI-H2452	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
nucleus	GO Cellular Component Annotations 2023	1.0	null
mRNA_RXRA_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
SNAI2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.1025
regulation of protein metabolic process	GO Biological Process Annotations 2015	1.0	null
FOSL1::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.958
NCI-H446	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
TC71	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.12169
HCC827GR5	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.41248
COV413A	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.33498
cell death	GO Biological Process Annotations 2015	1.0	null
HT	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.60635
KYSE-510	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.50322
biological_process	GO Biological Process Annotations 2015	1.0	null
EGR3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	52.9719
cervix, uterine	HPA Tissue Protein Expression Profiles	1.0	0.736095
BATF::JUN	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.7034
REH	CCLE Cell Line Gene CNV Profiles	1.0	1.41854
KMS-34	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
mRNA_ESX1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
mRNA_NR2F2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
regulation of apoptotic process	GO Biological Process Annotations 2023	1.0	null
TP53	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	28.9143
MHHES1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.77702
single-organism process	GO Biological Process Annotations 2015	1.0	null
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
T98G	Achilles Cell Line Gene Essentiality Profiles	1.0	2.01312
protein modification by small protein conjugation or removal	GO Biological Process Annotations 2015	1.0	null
HS729	CCLE Cell Line Gene CNV Profiles	1.0	1.62118
RARA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	58.1165
HCC2814	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.09305
MDA-MB-436	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
HLF	CCLE Cell Line Gene CNV Profiles	1.0	1.44563
programmed cell death	GO Biological Process Annotations 2015	1.0	null
THP1	Achilles Cell Line Gene Essentiality Profiles	1.0	1.35342
PMC11827247-41065_2025_387_MOESM5_ESM.xlsx-Sheet_1-Only_ESR_ESR1	Rummagene Transcription Factor Associations 2026	1.0	null
NCIH1650	Achilles Cell Line Gene Essentiality Profiles	1.0	1.70851
GSS	CCLE Cell Line Gene CNV Profiles	-1.0	-2.8155
NRL	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	35.5763
HUH7	CCLE Cell Line Gene CNV Profiles	1.0	1.3436
UMUC1	CCLE Cell Line Gene CNV Profiles	1.0	2.16729
stomach	HPA Tissue Protein Expression Profiles	1.0	0.736095
REC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00958
PAX1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.5633
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_9_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
intracellular organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
mRNA_AES_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
death	GO Biological Process Annotations 2015	1.0	null
PBX3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.9613
NCIH1341	CCLE Cell Line Gene CNV Profiles	1.0	1.45256
PU.1-20513432-BCELLS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
NCIH838	Achilles Cell Line Gene Essentiality Profiles	1.0	1.10248
BATF	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6179
cellular_component	GO Cellular Component Annotations 2015	1.0	null
FOSL2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.4861
NKX2-5	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.4245
deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
Decidua basalis	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.978
ZNF75A	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.6631
NCIH1693	CCLE Cell Line Gene CNV Profiles	1.0	1.69079
apoptotic process	GO Biological Process Annotations 2015	1.0	null
membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
HCC1493	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42358
cell part	LOCATE Predicted Protein Localization Annotations	1.0	null
NCIH2052	Achilles Cell Line Gene Essentiality Profiles	1.0	1.35945
intracellular part	GO Cellular Component Annotations 2015	1.0	null
ZNF528	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	48.7078
endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
cellular macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
ZSCAN4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	79.7269
CEBPB-20176806-MACROPHAGES-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
cellular_component	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
cytoplasmic part	GO Cellular Component Annotations 2015	1.0	null
HBL-100	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
PAX6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.7674
protein modification by small protein removal	GO Biological Process Annotations 2015	1.0	null
OPM-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
PK-8	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.54773
RT112	CCLE Cell Line Gene CNV Profiles	1.0	1.78257
regulation of macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
intracellular membrane-bounded organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
protein modification process	GO Biological Process Annotations 2015	1.0	null
Hyaluronan/mRNA-binding protein	InterPro Predicted Protein Domain Annotations	1.0	null
cerebellum	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
SK-MEL-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.37813
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
SK-MES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.00426
peptidase activity	GO Molecular Function Annotations 2015	1.0	null
SNU-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.38076
deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
G121	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.19603
TCF4-32651957-PLC/PRF/5-HUMAN-LIVER-HEPTOMA	ChEA Transcription Factor Targets 2022	1.0	null
Deubiquitination	Reactome Pathways 2024	1.0	null
Nuclear membrane protein complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.163
regulation of cellular process	GO Biological Process Annotations 2015	1.0	null
RT11284	CCLE Cell Line Gene CNV Profiles	1.0	1.34116
organelle	GO Cellular Component Annotations 2015	1.0	null
FOSL1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.8783
KASUMI1	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.26459
protein metabolic 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
intracellular part	LOCATE Predicted Protein Localization Annotations	1.0	null
EFO21	Achilles Cell Line Gene Essentiality Profiles	-1.0	-2.43492
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2023	1.0	null
SET2	CCLE Cell Line Gene CNV Profiles	-1.0	-1.47126
nucleus	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
CEBPA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.5585
VCAP	Achilles Cell Line Gene Essentiality Profiles	1.0	1.04728
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
KYSE-150	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
NCI-H2810	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.03948
nucleus	GO Cellular Component Annotations 2015	1.0	null
nucleus	GO Cellular Component Annotations 2025	1.0	null
hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
SNU16	CCLE Cell Line Gene CNV Profiles	-1.0	-1.49099
20460173-ImmPortComprehensiveListofImmune-RelatedGenes	GeneSigDB Published Gene Signatures	1.0	null
MHH-ES-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.02719
PKNOX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.4949
NCI-H1568	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
NCI-H2198	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
VMRCLCD	CCLE Cell Line Gene CNV Profiles	-1.0	-1.51354
regulation of cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
regulation of protein catabolic process	GO Biological Process Annotations 2015	1.0	null
mRNA_SFPI1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
HCC1395	CCLE Cell Line Gene CNV Profiles	-1.0	-2.68669
CFPAC-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
TOV21G	CCLE Cell Line Gene CNV Profiles	1.0	2.3175
pyrazinamide_mus musculus_gpl6246_gse48027	GEO Signatures of Differentially Expressed Genes for Small Molecules	-1.0	null
nucleus	LOCATE Predicted Protein Localization Annotations	1.0	null
ubiquitin-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
HCC366	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.04445
SIX2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	20.5454
NCI-H2171	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.2936
intracellular	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
regulation of cellular protein catabolic process	GO Biological Process Annotations 2015	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
A2058	Achilles Cell Line Gene Essentiality Profiles	1.0	1.10412
mRNA_EOMES_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
organic substance metabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
PL45	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
Peptidase C19, ubiquitin carboxyl-terminal hydrolase	InterPro Predicted Protein Domain Annotations	1.0	null
PMC9397613-can-21-1692_supplementary_table_s8_-_12_supps8-12.xlsx-S10_sgRNA-TP53_mutation_status-Unnamed_6_TP53	Rummagene Transcription Factor Associations 2026	1.0	null
WSU-NHL	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.79416
BCL6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.1172
PE01	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
ATF6	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.2986
HCC70	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.828501
Lipopolysaccharide receptor complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.889
proteasome-mediated ubiquitin-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
18614019-TableS4c	GeneSigDB Published Gene Signatures	1.0	null
biological regulation	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
NCI-H2009	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.42205
SNU-387	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.18444
regulation of proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
WIDR	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
MKN-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
cell part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
regulation of proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
TGIF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.7381
Post-translational protein modification	Reactome Pathways 2024	1.0	null
HCC1576	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
ZNF136	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	25.6404
HEP3B217	CCLE Cell Line Gene CNV Profiles	1.0	1.40745
SNU-C1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
SREBF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	33.156
mRNA_TUBA1A_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
PANC 02.03	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.0647
peptidase activity, acting on l-amino acid peptides	GO Molecular Function Annotations 2015	1.0	null
intracellular organelle	GO Cellular Component Annotations 2015	1.0	null
HOS	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65179
Metabolism of proteins	Reactome Pathways 2024	1.0	null
SH10TC	CCLE Cell Line Gene CNV Profiles	-1.0	-2.1676
K029AX	CCLE Cell Line Gene CNV Profiles	-1.0	-1.3543
Ubiquitin specific protease, conserved site	InterPro Predicted Protein Domain Annotations	1.0	null
HS 69ST	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.964955
epididymis	HPA Tissue Protein Expression Profiles	1.0	1.32926
OVKATE	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.66825
NELF complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.753
LXF-289	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
protein modification by small protein removal	GO Biological Process Annotations 2023	1.0	null
KELLY	CCLE Cell Line Gene CNV Profiles	-1.0	-1.38038
HCC-15	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.09303
CA SKI	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14515
mRNA_SMAD1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
urinary bladder	HPA Tissue Protein Expression Profiles	1.0	1.32926
cell part	GO Cellular Component Annotations 2015	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2025	1.0	null
Microtubule organizing center attachment site	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.143
NCI-H522	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.893239
modification-dependent protein catabolic process	GO Biological Process Annotations 2015	1.0	null
KAP1-22055183-ESCS-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
mRNA_CDX2_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
TK	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
LN-18	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
NCI-H1915	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.69525
KP3	CCLE Cell Line Gene CNV Profiles	1.0	1.66062
MDA-MB-468 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.053
protein deubiquitination	GO Biological Process Annotations 2023	1.0	null
catabolic process	GO Biological Process Annotations 2015	1.0	null
protein deubiquitination	GO Biological Process Annotations 2015	1.0	null
OVKATE	CCLE Cell Line Gene CNV Profiles	1.0	2.07461
KALS1	Achilles Cell Line Gene Essentiality Profiles	1.0	1.06388
TGBC11TKB	CCLE Cell Line Gene CNV Profiles	-1.0	-1.66854
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
ubiquitin-like protein-specific protease activity	GO Molecular Function Annotations 2015	1.0	null
mRNA_TCF3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
RT-112	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	2.17725
DSIF complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	0.875
IGR39	Achilles Cell Line Gene Essentiality Profiles	1.0	1.24108
PAX9	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.5658
CAPAN-2	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.14664
mRNA_DLX3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
mRNA_NRIP1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
ECC12	CCLE Cell Line Gene CNV Profiles	-1.0	-2.05819
ZR-75-1 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.682
CEBPD	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	29.1787
cell	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
SUPHD1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.81586
BT474	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.1448
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
proteasomal protein catabolic process	GO Biological Process Annotations 2015	1.0	null
RERFLCAD1	CCLE Cell Line Gene CNV Profiles	1.0	2.04563
TCF7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8627
PK-45P	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.28598
NCIH1651	CCLE Cell Line Gene CNV Profiles	1.0	1.33471
cellular macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
JK1	CCLE Cell Line Gene CNV Profiles	-1.0	-1.37771
NCI-H1373	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.23641
vitamin c_mus musculus_gpl6246_gse19377	GEO Signatures of Differentially Expressed Genes for Small Molecules	-1.0	null
COLO205	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.39572
G61	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
ELK1::HOXA1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.6492
HSF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.0547
U343	CCLE Cell Line Gene CNV Profiles	1.0	1.70306
ubiquitin-dependent protein catabolic 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
mRNA_NANOG_16518401	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
18614019-TableS4d	GeneSigDB Published Gene Signatures	1.0	null
macromolecule modification	GO Biological Process Annotations 2015	1.0	null
HCC2279	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.21283
NCI-H2196	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
Viral meningitis	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.004
NB4	CCLE Cell Line Gene CNV Profiles	1.0	1.44418
LN443	Achilles Cell Line Gene Essentiality Profiles	1.0	2.53393
EFM-192B	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
cytoplasmic part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
BICR 22	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.65384
endoplasmic reticulum	GO Cellular Component Annotations 2015	1.0	null
single-organism cellular process	GO Biological Process Annotations 2015	1.0	null
OSR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	18.3567
SW1710	CCLE Cell Line Gene CNV Profiles	1.0	2.49101
EBF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	40.9225
HCC1500	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
BT-549 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.236
PMC8242083-41467_2021_24064_MOESM4_ESM.txt--HSF1_HSF1	Rummagene Transcription Factor Associations 2026	1.0	null
E2F7	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8265
proteolysis	GO Biological Process Annotations 2015	1.0	null
FU97	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
NCIH1436	CCLE Cell Line Gene CNV Profiles	-1.0	-1.55493
SK23	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
mRNA_SMAD7_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
MOLM-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-1.14434
Ub-specific processing proteases	Reactome Pathways 2024	1.0	null
regulation of programmed cell death	GO Biological Process Annotations 2023	1.0	null
SPI1-20176806-THIOMACROPHAGE-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
intracellular part	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
NCI-H2803	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.905023
NKX3-2	JASPAR Predicted Transcription Factor Targets	1.0	null
NCI-H2122	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.889738
Nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.189
PRDM1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	23.6534
SKNMC	CCLE Cell Line Gene CNV Profiles	-1.0	-1.46058
cellular_component	LOCATE Predicted Protein Localization Annotations	1.0	null
membrane-bounded organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
mRNA_KLF4_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
HCC827	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.75604
HCC4006	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	144.621
NCI-H1693	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
organic substance catabolic process	GO Biological Process Annotations 2015	1.0	null
HCC2279	CCLE Cell Line Gene CNV Profiles	1.0	1.55036
MG-63	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.977474
MDA-MB-453 cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.646
SUM cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	0.98
HCC2218	CCLE Cell Line Gene CNV Profiles	-1.0	-1.58846
cellular metabolic process	GO Biological Process Annotations 2015	1.0	null
496100595_PCx_probable Alzheimer's disease_no TBI_95-99_F	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	17.5796
CEBPB-20513432-MACROPHAGES-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
USF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	26.8105
C32	Achilles Cell Line Gene Essentiality Profiles	1.0	1.60557
LN235	Achilles Cell Line Gene Essentiality Profiles	1.0	1.05024
modification-dependent macromolecule catabolic process	GO Biological Process Annotations 2015	1.0	null
HCC1806	CCLE Cell Line Gene CNV Profiles	-1.0	-1.95376
SPI1	ChEA Transcription Factor Targets	1.0	null
mRNA_SALL4_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
RREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	238.909
TGIF2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.5859
HGC-27	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
CEBPG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	32.6525
proteolysis involved in cellular protein catabolic process	GO Biological Process Annotations 2015	1.0	null
intracellular organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
regulation of apoptotic process	GO Biological Process Annotations 2025	1.0	null
MSANTD3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	21.0034
PMC6604319-13072_2019_278_MOESM3_ESM.xlsx-CEM_ect_TET2_DEGs_DMRs_hDMRs-Unnamed_1_TET2	Rummagene Transcription Factor Associations 2026	1.0	null
protein catabolic process	GO Biological Process Annotations 2015	1.0	null
NCI-H1781	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.1248
mRNA_GATA3_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
EGR1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	83.2503
ubiquitinyl hydrolase activity	GO Molecular Function Annotations 2015	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2025	1.0	null
primary metabolic process	GO Biological Process Annotations 2015	1.0	null
HLFA	CCLE Cell Line Gene CNV Profiles	1.0	1.70338
membrane-bounded organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
catalytic activity	GO Molecular Function Annotations 2015	1.0	null
CREB1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.6179
NKX2-3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.7198
NCIH1373	CCLE Cell Line Gene CNV Profiles	1.0	1.42321
ZFP42	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	30.6176
ovary	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
DB	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.976613
NCIH358	CCLE Cell Line Gene CNV Profiles	1.0	1.33632
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2015	1.0	null
macromolecule 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
NCI-N417	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
NIH:OVCAR-3	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.983025
liver	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
PK-59	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
endoplasmic reticulum	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
C2BBE1	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.14418
regulation of cellular protein metabolic process	GO Biological Process Annotations 2015	1.0	null
HS695T	CCLE Cell Line Gene CNV Profiles	1.0	1.73114
GTL-16	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
NCI-H1770	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.6208
Pancreatic ductal carcinoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.383
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2025	1.0	null
intracellular membrane-bounded organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2023	1.0	null
NR2F2	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.9564
parathyroid gland	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
macromolecule metabolic process	GO Biological Process Annotations 2015	1.0	null
MFM-223	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.00171
786-O	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.829994
SKM-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.82084
mRNA_CBX8_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
ETS1-21867929-TH2-MOUSE	ChEA Transcription Factor Targets 2022	1.0	null
HSF1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.2129
RMG-I	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.72314
rosiglitazone_mus musculus_gpl7202_gse19896	GEO Signatures of Differentially Expressed Genes for Small Molecules	1.0	null
regulation of catabolic process	GO Biological Process Annotations 2015	1.0	null
molecular_function	GO Molecular Function Annotations 2015	1.0	null
MYOD1	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	31.3781
JEKO-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
H322T	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.52074
KNS62	CCLE Cell Line Gene CNV Profiles	-1.0	-1.86965
G111	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.53906
CAKI-1	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.34595
SUM-159PT cell	TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025	1.0	1.183
endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
HS852T	CCLE Cell Line Gene CNV Profiles	-1.0	-1.48869
lateral ventricle	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
organelle	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
KNS-62	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.46108
G-361	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.922577
rectum	HPA Tissue Protein Expression Profiles	1.0	1.32926
NCI-H1435	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
Childhood osteosarcoma	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	1.0	1.118
FOXP3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.599
NCI-H358	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
prostate	HPA Tissue Protein Expression Profiles	1.0	1.32926
hippocampus	HPA Tissue Protein Expression Profiles	-1.0	-1.44517
PRC_Partial Depletion_GDS3531_563_human_U2OS cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
mRNA_MYC_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	-1.0	null
cerebral cortex	HPA Tissue Protein Expression Profiles	-1.0	-0.903885
TGIF2LX	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	22.4583
PRC_DEPLETION_GDS3532_96_human_U2OS cells	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	-1.0	null
JHH-7	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-0.866072
cytoplasm	COMPARTMENTS Curated Protein Localization Evidence Scores	1.0	0.098109
HCC1395	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	-1.0	-2.39131
organelle	LOCATE Predicted Protein Localization Annotations	1.0	null
AM38	Achilles Cell Line Gene Essentiality Profiles	1.0	1.26593
RMUG-S	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	0.828822
regulation of metabolic process	GO Biological Process Annotations 2015	1.0	null
AGS	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.34617
RARA::RXRG	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	41.2992
EGR4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	89.9066
496100560_PCx_no dementia_TBI_87_M	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	1.0	7.70819
BATF3	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	16.8567
cysteine-type deubiquitinase activity	GO Molecular Function Annotations 2025	1.0	null
SPI1-20176806-THIOMACROPHAGE-MOUSE	ChEA Transcription Factor Binding Site Profiles	1.0	null
NCI-H187	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.54068
COLO 320DM	Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles	1.0	1.30674
PANC1005	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.37746
cysteine-type peptidase activity	GO Molecular Function Annotations 2023	1.0	null
mRNA_MYOD1_19796622	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	1.0	null
cysteine-type peptidase activity	GO Molecular Function Annotations 2015	1.0	null
cellular process	GO Biological Process Annotations 2015	1.0	null
cysteine-type endopeptidase activity	GO Molecular Function Annotations 2015	1.0	null
Meiotic nuclear membrane microtubule tethering complex	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	1.0	1.189
TP73	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	17.2211
regulation of biological process	GO Biological Process Annotations 2015	1.0	null
SKBR3	CCLE Cell Line Gene CNV Profiles	-1.0	-1.65369
E2F4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	15.0624
regulation of primary metabolic process	GO Biological Process Annotations 2015	1.0	null
intracellular membrane-bounded organelle	GO Cellular Component Annotations 2023	1.0	null
cellular protein modification process	GO Biological Process Annotations 2015	1.0	null
regulation of cellular catabolic process	GO Biological Process Annotations 2015	1.0	null
LNZ308	Achilles Cell Line Gene Essentiality Profiles	-1.0	-1.04454
ATF4	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	19.8282
RARA::RXRA	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	44.087
regulation of proteolysis	GO Biological Process Annotations 2015	1.0	null
fallopian tube	HPA Tissue Protein Expression Profiles	1.0	1.32926
FOSL2::JUNB	JASPAR Predicted Human Transcription Factor Targets 2025	1.0	24.599