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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

  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
  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
  brown 195 Anatomical structure morphogenesis Leukocyte transendothelial migration 5 TMOD3, CREB1, POU5F1, SP3, TERT
  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
  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
  magenta 26 Regulation of metabolic process p53 signaling pathway, Alzheimer's disease 3 ATF6, NGEF, POGK
  pink 30 Transcription initiation from RNA polymerase II promoter Basal transcription factors 4 CCDC92, TMEM70, RNF139, E2F5
  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
  turquoise 295 Regulation of cellular metabolic process p53 signaling pathway, Pancreatic cancer, Apoptosis 2 UBL5, RNF111
  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
  Total 1317     
miRNA-mRNA interactions Genes Gene count Top GO category Top KEGG categories Key driver count Key drivers
   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
  miRNAs miRNA count Top functional categories Top HMDD categories Key driver count Key drivers
   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
  1. For the 10 gene modules identified in TF-mRNA interactions, we list counts of the involved genes, the most significant GO and KEGG terms, and the identified key driver genes from each module. Similarly for the miRNA-mRNA interactions, we list the key driver molecules of both genes and miRNAs. The driver genes, whose protein products are known to be targeted by drugs, are in bold.