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Table 4 Predicted protein complexes, their GO-terms, p-values, and KEGG pathways

From: A multiobjective approach for identifying protein complexes and studying their association in multiple disorders

Sl.No. Cluster id Predicted complex (% of proteins covered) Matched proteins GO-term (bp) GO-term (CC) GO-term (mf) KEGG pathway
1 5 CTNNB1–DVL1–DVL3–PPM1A complex (80%), HSPB1–PPA1–PPA1–SETDB1–TP53–WIPI1 complex (66.67), EEF1A1–MDH2–WARS complex (66.67), transforming growth factor–SMAD complex (66.67) DVL2, ‘CTNNB1’ ‘PPM1A’ ; ‘SMAD3’ ‘TP53’ ‘PPA1’ ‘PPA1’; YWHAG’ ‘EEF1A1’; ‘EEF1A1’ ‘SMAD2’ Enzyme linked receptor protein signaling pathway (GO:0007167 ) (5.9E–11) Cytosol (GO:0005829) (3.4E–11) Enzyme binding (GO:0019899) (1.5E–12) Colorectal cancer (2.9E–11), Pathways in cancer(1.2E–10)
2 6 CDH1–CTNNB1–PTPN1 complex(50), transforming growth factor–SMAD complex (66.67), HSPB1–PPA1–PPA1–SETDB1–TP53–WIPI1 complex (66.67) DVL2 SMAD3 TP53 YWHAG Response to organic substance (GO:0010033) (4.2E–14) Cytosol (GO:0005829) (2.5E–25) Protein kinase activity (GO:0004672) (1.8E–10) Pathways in cancer (6.1E–19)
3 8 MARCKS–NMT1–TP53 complex (66.67), transforming growth factor–SMAD complex (75), CTNNB1–DVL1–DVL3–PPM1A complex (50) CTNNB1 SMAD3 TP53 YWHAG TP53 SMAD2 Protein amino acid phosphorylation (GO:0006468) (4.1E–14) Cytosol (GO:0005829) (3.8E–23) Protein serine/threonine kinase activity (GO:0004674) (1.7E–11) Chronic myeloid leukemia (5.7E–16)
4 11 p300–MDM2–p53 protein complex (63.64), CDH1–CTNNB1–PTPN1 complex (60) HDAC1 TP53 ESR1 TP53 CTNNB1 Positive regulation of nitrogen compound metabolic process (GO:0051173) (4.1E–20) Nucleoplasm (GO:0005654) (2.6E–18) Transcription factor binding (GO:0008134) (1.5E–15) Prostate cancer (2.0E–12)
5 15 p300–MDM2–p53 protein complex (72.73), CASP8–MAPK1–MAPK3–PEA15–RPS6KA3 complex (60),CDH1–CTNNB1–PTPN1 complex (75), EP300–HOXB6–HOXB7 complex (66.67) EP300 HDAC1 TP53 ESR1 LCK HSP90AA1 MAPK1 MAPK3 EP300 TP53 EP300 TP53 FOXO1 SMAD4 EP300 SMAD2 CTNNB1 PTPN1 HGS EP300 EEF1A1 SMAD2 Positive regulation of macromolecule metabolic process (GO:0010604) (4.5E–34) Nucleoplasm (GO:0005654) (3.1E–34) Transcription regulator activity (GO:0030528) (7.6E–26) Chronic myeloid leukemia (9.1E–26)
6 20 Smad protein complex (53.33), FOXO–SMAD complex (60), transforming growth factor–SMAD complex (75), CDH1–CTNNB1–PTPN1 complex (75) SMAD3 SMAD2 LCK HSP90AA1 TP53 YWHAG CTNNB1 SMAD2 Positive regulation of cellular biosynthetic process (GO:0031328) (6.8E–23) Cytosol (GO:0005829) (3.9E–15) Enzyme binding (GO:0019899) (1.5E–20) Adherens junction (1.2E–16)
7 25 EEF1A1–MDH2–WARS complex (66.67), CTNNB1–DVL1–DVL3–PPM1A complex (66.67) DVL2 CTNNB1 PPM1A SMAD3 TP53 PPA1 PPA1 YWHAG EEF1A1 EEF1A1 SMAD2 Enzyme linked receptor protein signaling pathway (GO: 0007167) (2.5E–15) Cytosol (GO:0005829) (6.1E–20) SMAD binding (2.2E–13) (GO:0046332) Pathways in cancer (3.5E–21)
8 26 CDK5R2–CHN1–ERBB2 complex (66.67), EEF1A1–MDH2–WARS complex(66.67) SMAD3 TP53 YWHAG SMAD2 Response to organic substance (GO:0010033) (4.9E–12) Cytosol (GO:0005829) (3.9E–20) Enzyme binding (GO:0019899) (8.0E–16) Colorectal cancer(6.4E–14)
9 36 SMAD1–SMAD4–ECSIT2 containing complex (80), CDH1–CTNNB1–PTPN1 complex (75), p300–MDM2–p53 protein complex (81.82) ‘BRCA1’ ‘CTNNB1’ ‘ECSIT’ ‘EP300’ ‘ESR1’ ‘HDAC1’ ‘MDM2’ ‘PTPN1’ ‘RB1’ ‘SMAD1’ ‘SMAD4’ ‘SP1’ ‘TP53’ ‘UBE2Z’ Positive regulation of cellular biosynthetic process (GO:0031328) (7.8E–37) Nuclear lumen (GO:0031981) (3.0E–27) Transcription regulator activity (1.7E–30) (GO:0030528) Pathways in cancer(2.6E–30)
10 39 FOXO–SMAD complex (60), EEF1A1–MDH2–WARS complex (66.67), CDH1–CTNNB1–PTPN1 complex (75) ‘CDH2’ ‘CTNNB1’ ‘EEF1A1’ ‘FOXO1’ ‘FOXO3’ ‘SMAD1’ ‘SMAD4’ ‘YWHAG’ Cell cycle (GO:0007049) (1.2E–30) Nucleoplasm (GO:0005654) (8.8E–59) Transcription factor binding (GO:0008134) (1.5E–25) Cell cycle (1.6E–18)
11 40 ERBB2IP–ZFYVE9 containing complex, p300–MDM2–p53 protein complex (72.73), CDK7–cyclin H complex (60) ‘AR’ ‘BRCA1’ ‘CDK2’ ‘EP300’ ‘ERBB2IP’ ‘ESR1’ ‘HDAC1’ ‘MDM2’ ‘MNAT1’ ‘SP1’ ‘TBP’ ‘TP53’ ‘UBE2I’ Positive regulation of macromolecule metabolic process (GO:0010604) (1.6E–29) Nuclear lumen(GO:0031981) (1.3E–19) Transcription activator activity (GO:0016563) (3.2E–14) Pathways in cancer(3.3E–16)
12 10 CDK7–cyclin H complex (80), CASP8–MAPK1–MAPK3–PEA15–RPS6KA3 complex (80), ITPR1–STARD13–TXNDC4 complex (66.67), PIN1–TP53 complex(66.67) ‘AR’ ‘CASP8’ ‘CDK2’ ‘CDK7’ ‘HMGB1’ ‘ITPR1’ MAPK1’ ‘MAPK3’ ‘MDM2’ ‘MNAT1’ ‘PEA15’ ‘PIN1’ ‘TP53’ ‘TP73’ Positive regulation of gene expression (GO:0010628) (1.0E–23) Transcription factor complex (GO:0005667) (9.8E–13) Enzyme binding (GO:0019899) (9.7E–21) Pathways in cancer (7.0E–26)
13 51 HSPA1A–TP53 complex (100), ATXN1–C1orf94–DAZAP2–RBPMS–UBQLN4 containing complex (66.67), p300–MDM2–p53 protein complex (80) ‘ATXN1’ ‘BAT2’ ‘BRCA1’ ‘DAZAP2’ ‘EP300’ ‘ERBB2IP’ ‘ESR1’ ‘HDAC1’ ‘HSPA1A’ ‘MDM2’ ‘SP1’ ‘TBP’ ‘TP53’ ‘UBE2I’ ‘UBQLN4’ Positive regulation of cellular biosynthetic process (GO:0031328) (4.7E–32) Nucleoplasm (GO:0005654) (1.7E–28) Transcription regulator activity (GO:0030528) (3.2E–20) Pathways in cancer (4.2 E–24)
14 3 CDH1–CTNNB1–PTPN1 complex (75), EEF1A1–MDH2–WARS complex(66.67) ‘CDH2’ ‘CTNNB1’ ‘EEF1A1’ ‘PTPN1’ ‘YWHAG’ Positive regulation of macromolecule metabolic process (GO:0010604) (8.7E–28) Nucleoplasm (GO:0005654) (2.0E–18) Transcription factor binding (GO:0008134) (1.3E–18) Neurotrophin signaling pathway (2.3E–12)
15 38 COP9 signalosome (CSN) (70), mutant p53/NF-Y protein (mutp53/NF-Y) complex (66.67), TP53–TP73 complex (66.67), HSPB1–PPA1–PPA1–SETDB1–TP53–WIPI1 complex (66.67) ‘COPS3’ ‘COPS4’ ‘COPS5’ ‘COPS6’ ‘COPS7A’ ‘COPS8’ ‘CREBBP’ ‘EP300’ ‘GPS1’ ‘NFYA’ ‘PPA1’ ‘SMAD3’ ‘SP1’ ‘TP53’ ‘TP73’ ‘WT1’ Positive regulation of nitrogen compound metabolic process (GO:0051173) (6.9E–22) Cytosol (GO:0005829) (1.4E–10) Enzyme binding (GO:0019899) (2.8E–18) Pathways in cancer (7.0E–20)
16 21 MDM2–PML–PML–SUMO1–SUZ12 complex (80), SUMO1 activation complex (66.67), p300–MDM2–p53 protein complex (80) ‘AR’ ‘BRCA1’ ‘DAXX’ ‘EP300’ ‘ESR1’ ‘HDAC1’ ‘MDM2’ ‘PIAS1’ ‘PML’ ‘RB1’ ‘SP1’ ‘SUMO1’ ‘TP53’ ‘UBE2I’ Positive regulation of transcription (5.7E–34) Organelle lumen (GO:0043233) (8.3E–34) Transcription regulator activity (GO:0030528) (4.9E–39) Pathways in cancer (3.9E–21)
17 30 CDH1–CTNNB1–PTPN1 complex (75), PKD1–PKD2 complex (66.67), EEF1A1–MDH2–WARS complex (66.67) ‘CDH2’ ‘CTNNB1’ ‘EEF1A1’ ‘PKD1’ ‘PTPN1’ ‘YWHAG’ Positive regulation of nitrogen compound metabolic process (GO:0051173) (1.0E–17) Cell projection (GO:0042995) (9.0E–8) Enzyme binding (GO:0019899) (2.1E–13) Adherens junction (1.5E–18)
18 13 TP53–TP73 complex (66.67), p300–MDM2–p-53 protein complex (72.73) ‘BRCA1’ ‘CREBBP’ ‘EP300’ ‘ESR1’ ‘HDAC1’ ‘MDM2’ ‘SP1’ ‘TBP’ ‘TP53’ ‘TP73’ ‘WT1’ Positive regulation of cellular biosynthetic process (GO:0031328) (3.1E–25) Nuclear lumen (7.3E–24) Transcription regulator activity (GO:0030528) (2.2E–24) Prostate cancer (8.5E–9)