Table 3 Highly connected modules identified at PPI networks and enrichment analysis of each module
Subnetwork A (TT vs. NT) | |||
|---|---|---|---|
Module | Genes | KEGG pathways | p-value |
Module 1 | ANLN, BUB1, CCNA2, CCNB1, CCNB2, CCND1, CCNE2 CDK1, CDKN2A, CDKN2C, CDKN3, CKS2, DLGAP5, E2F3, ECT2, FOXM1, KIF11, KIF20A, KIF23, MELK, MKI67, NCAPG, NUF2, PARP1, PLK1, PRC1, RACGAP1, RRM2, RRM2B, SMC4, SNCG, SPC25, TOP2A, TP63, TPX2, TTK, ZWINT | Cell cycle Cellular senescence p53 signaling pathway Viral carcinogenesis Pathways in cancer | 7.75E-67 8.59E-26 3.81E-23 3.56E-19 1.25E-12 |
Module 2 | ARHGAP35, BLNK, CAV1, CAV2, CDH1, CLEC3B, CTNNA1, EGFR, ERBB3, FNBPIL, GRB2, KALRN, KIT, MET, MME, MMP9, NRG1, PDGFD, PIK3R1, PIK3R3, PREX1, PTPRJ, SGIP1, SORBS1, SPRY1 SPRY2, TNS1, VEGFC | ErbB signaling pathway EGFR tyrosine kinase inhibitor resistance Focal adhesion Ras signaling pathway Proteoglycans in cancer | 2.95E-47 1.13E-39 1.68E-36 3.57E-36 2.08E-28 |
Module 3 | ACVR1C, AMOTL1, AR, CDH11, CDH3, ESR1, EZH1, EZH2, FOXA1, HDAC1, NCOA7, NR3C1, PPARG, PPARGC1A, RUNX2, SKIL, SNAI2, SOX6, STMN1, VTCF7L2, THRA, TLE4, ZBTB16, ZEB2 | Transcriptional misregulation in cancer Thyroid hormone signaling pathway Pathways in cancer Signaling pathways regulating pluripotency of stem cells Adherens junction | 1.02E-14 1.30E-11 4.54E-11 1.91E-08 2.78E-07 |
Subnetwork B (PT vs. NT) | |||
Module | Genes | KEGG pathways | p-value |
Module 1 | ANLN, ARHGAP11A, BUB1, CCND1, CCNF, CDK1, CDKN2A, CDKN2C CDKN3, CENPF, DLGAP5, E2F3, KIF18A, KIF20A, KIF23, MKI67, PRC1, RCC2, RRM2, SNCG, TOP2A, TTK | Cell cycle Viral carcinogenesis Cellular senescence p53 signaling pathway Steroid hormone biosynthesis | 2.27E-77 9.98E-21 1.51E-16 1.05E-15 8.53E-07 |
Module 2 | ADGRA2, CAV1, CAV2, CDH11, DLG5, DOCK10, FN1, GSN, KALRN, MET, NTRK2, NTRK3, PAK3, PRKAR2B, PTPRJ, RAB4B, S100A4, SORBS1, SPINT2, TCN1 TNS1, VCAN | Focal adhesion Ras signaling pathway Proteoglycans in cancer PI3K-Akt signaling pathway Regulation of actin cytoskeleton | 8.44E-42 1.97E-34 1.18E-30 4.22E-26 4.45E-25 |
Module 3 | BMPR1B, CHRDL1, INHBA, RGMA, SOSTDC1, TFGBR1, TGFBR3 | TGF-beta signaling pathway Hippo signaling pathway Cytokine-cytokine receptor interaction Signaling pathways regulating pluripotency of stem cells Steroid hormone biosynthesis | 2.91E-51 1.63E-16 4.34E-16 2.84E-10 8.09E-10 |