Table 1 The key driver elements identified TF-gene interactions and miRNA-mRNA interactions.
From: Integrative network-based approach identifies key genetic elements in breast invasive carcinoma
| Â | Module | Gene count | Top GO category | Top KEGG categories | Key driver count | Key drivers |
|---|---|---|---|---|---|---|
TF-mRNA interactions | black | 41 | Regulation of transcription | Pathways in cancer, Renal cell carcinoma | 5 | SORBS3, ZNF43, ZNF681, RBMX, POU2F1 |
| Â | blue | 247 | Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | Cell cycle, Prostate cancer, Melanoma | 9 | AR, BRCA1, ESR1, JUN, MYB, RPN1, E2F1, E2F2, PPARD |
| Â | brown | 195 | Anatomical structure morphogenesis | Leukocyte transendothelial migration | 5 | TMOD3, CREB1, POU5F1, SP3, TERT |
| Â | green | 110 | Cellular macromolecule metabolic process | Endometrial cancer, Insulin signaling pathway | 15 | B4GALT7, OS9, CDC34, MAN2C1, MYO1C, SH3GLB2, INPP5E, PLXNB1, USF2, PPP1R12C, CDK9, DAP, E4F1, E2F4, USF1 |
| Â | grey | 148 | Anatomical structure development | Sulfur metabolism | 18 | AHCTF1, NQO2, FGFR2, CCDC130, ABCG4, BIRC6, CA6, SP4, RNF2, SPRR1B, C16orf65, DNAJC5G, SNCAIP, GRIK5, SLC6A4, SMAD1, DAD1, POU4F2 |
| Â | magenta | 26 | Regulation of metabolic process | p53 signaling pathway, Alzheimer's disease | 3 | ATF6, NGEF, POGK |
| Â | pink | 30 | Transcription initiation from RNA polymerase II promoter | Basal transcription factors | 4 | CCDC92, TMEM70, RNF139, E2F5 |
| Â | red | 93 | Regulation of cellular process | Endometrial cancer, Neurotrophin signaling pathway | 14 | ATP1B1, STAT3, ABCB8, MYC, TGFB1, SP1, TP53, PCGF1, SUMF2, GTF3A, IPO13, GMPPA, HTR6, TGIF1 |
| Â | turquoise | 295 | Regulation of cellular metabolic process | p53 signaling pathway, Pancreatic cancer, Apoptosis | 2 | UBL5, RNF111 |
| Â | yellow | 132 | Immune system process | Chemokine signaling pathway, Natural killer cell mediated cytotoxicity | 19 | APOC1, CD2, CD79B, LRRC28, DAPK1, FAM124B, EML2, LAP3, TSPAN2, FCRL3, ELMO1, SLC7A7, RASSF5, SLC31A2, TRAF3IP3, GALNT12, ITGA4, SPI1, TFAP2A |
| Â | Total | 1317 | Â | Â | Â | Â |
miRNA-mRNA interactions | Genes | Gene count | Top GO category | Top KEGG categories | Key driver count | Key drivers |
| Â | Â | 869 | Regulation of macromolecule metabolic process | Pathways in cancer, Pancreatic cancer, Prostate cancer | 17 | MYC, ATG4C, TGFB1, NFKB1, AKT1, EGR1, TP53, SOX10, SPI1, MECP2, E2F3, CREB1, TCF3, TPP1, FLICE, LPS, PACS1 |
| Â | miRNAs | miRNA count | Top functional categories | Top HMDD categories | Key driver count | Key drivers |
| Â | Â | 120 | miRNA tumor suppressors, immune response, Onco-miRNA, cell death, human embryonic stem cells regulation | Breast cancer (65), Neoplasms (58), Melanoma (56), Ovarian Neoplasms (51), Pancreatic Neoplasms (38), Prostatic Neoplasms (38) | 68 | mir-126, mir-609, mir-488, mir-191, mir-200c, mir-200a, mir-30a, mir-30d, mir-335, mir-190b, mir-223, mir-106b, mir-519e, mir-210, mir-379, mir-203, mir-205, mir-708, mir-29c, mir-29a, mir-182, mir-183, mir-127, mir-187, mir-425, let-7g, let-7d, mir-152, mir-155, mir-21, mir-22, mir-758, mir-921, mir-922, mir-375, mir-377, mir-181a-2, mir-657, mir-302d, mir-100, mir-10b, mir-10a, mir-625, mir-629, mir-92a-2, mir-26b, mir-25, mir-145, mir-143, mir-141, mir-221, mir-193b, mir-193a, mir-374a, mir-134, mir-146a, mir-31, let-7a-2, mir-27a, mir-27b, mir-133a-1, let-7i, mir-93, mir-23a, mir-148a, mir-196a-2, mir-487b, mir-149 |