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