Table 3.
Hub genes as obtained from cytoHubba and MCODE plugins of Cytoscape.
| A. Genes Included in the Final Ranked List Aggregated from the 10 Topological cytoHubba Methods | |||
|---|---|---|---|
| IL6, VEGFA, CCNB1, BRCA1, CCNA2, CD44, TYMS, CDH1, LMNB1, AURKB, EZH2, MKI67, KIF23, ECT2, MCM4, CDC6, PLK1, CDC25C, CDKN3, CENPA, MMP2, TOP2A, CENPE, PBK, NDC80, FOXM1, SPP1, IGF1, UBE2C, RRM2, KIF11, CHEK1, CD8A, CCNB2, ASPM, NCAM1, FLNA, LGALS4, ITPR1, DLGAP5, CDCA8, COL5A1, TIMELESS, CDC20, DMD, PPARGC1A, WNT5A, BUB1, KIF20A, EXO1, CDC25A, VCL, LUM, CCND2, CD34, MCM2, MAD2L1, HPGDS, ISL1, ESRP1, SKP2, NCAPG, CENPU, HJURP, CCL2, TPM1, CDH11, PLK4, FABP4, H2AFX, GJA1, DHCR7, PTGS2, MSN, ANXA5, COL6A1, TRIP13, OIP5, MYH11, KRT20, TTK, MYL9, CAV1, FBXO5, PROM1, BMP4, CDT1, KIAA0101, CCNE1, ANXA1, FGFR3, SNCA, ATAD2, ESPL1, FASN, NT5E, ZWINT, SDC1, FGF2, NEK2, ACTG2, KIF14, COL3A1, EPCAM, ASF1B, IGFBP5, RAD54L, CYP1B1, STMN1, COL4A5, ATF3, CASC5, CENPM, ERBB3, DNMT3B, ITGB2, ISG15, ANK2, CDC45, PLAT, TACC3, EGR1, MYLK, CTSG, GINS2, ITGA8, CENPF, TGFBR2, OGN | |||
| B. Genes included in the first three clusters of MCODE | |||
| Cluster | Score | Nodes | Gene clusters |
| 1 | 74.268 | 83 | PLK4, TRIP13, CDC45, PBK, RRM2, ERCC6L, CHAF1A, DEPDC1, DLGAP5, ASPM, E2F8, MAD2L1, CDCA8, CCNB1, BRCA1, FANCI, FBXO5, CENPA, KIAA0101, TK1, TACC3, DTL, CDCA3, HJURP, CENPE, ZWINT, ESPL1, POLQ, OIP5, CDC25C, ASF1B, CDKN3, POLE2, CCNB2, CHAF1B, EZH2, UBE2C, RAD54L, CDT1, MCM5, CDC20, TROAP, CKS2, NEK2, SPC25, MKI67, CHEK1, TTK, CDC6, GINS2, BUB1, CENPU, CCNE2, STIL, KIF14, TYMS, CDC7, MCM2, KIF23, KNTC1, SKA1, CASC5, CENPF, HELLS, NUSAP1, ATAD2, CEP55, NCAPG, MCM4, NDC80, ECT2, TOP2A, CENPM, CDC25A, MCM10, ORC1, KIF20A, AURKB, CCNA2, PLK1, EXO1, FOXM1, KIF11 |
| 2 | 18 | 23 | CXCL12, PTGS2, BMP4, IL6, GJA1, CD34, FGF2, NES, PROM1, CD8A, VEGFA, CD44, SDC1, SPP1, ANXA5, NCAM1, SELP, CCL2, CCL5, IGF1, CSF1R, NT5E, SELE |
| 3 | 7.923 | 27 | TGFBI, COL6A2, THBS2, TPM1, MYH11, ACTG2, COL6A1, COL13A1, COL3A1, TGFBR2, VCL, FBLN2, COL4A5, CTSK, LYVE1, CLDN5, ANGPT2, LUM, MYL9, LEPREL1, TPM2, SPARC, MYLK, CAV1, ADAMTS5, TAGLN, FMOD |
| C. Common genes between cytoHubba and MCODE | |||
| IL6, VEGFA, CCNB1, BRCA1, CCNA2, CD44, TYMS, AURKB, EZH2, MKI67, KIF23, ECT2, MCM4, CDC6, PLK1, CDC25C, CDKN3, CENPA, TOP2A, CENPE, PBK, NDC80, FOXM1, SPP1, IGF1, UBE2C, RRM2, KIF11, CHEK1, CD8A, CCNB2, ASPM, NCAM1, DLGAP5, CDCA8, CDC20, BUB1, KIF20A, EXO1, CDC25A, VCL, LUM, CD34, MCM2, MAD2L1, NCAPG, CENPU, HJURP, CCL2, TPM1, PLK4, GJA1, PTGS2, ANXA5, COL6A1, TRIP13, OIP5, MYH11, TTK, MYL9, CAV1, FBXO5, PROM1, BMP4, CDT1, KIAA0101, ATAD2, ESPL1, NT5E, ZWINT, SDC1, FGF2, NEK2, ACTG2, KIF14, COL3A1, ASF1B, RAD54L, COL4A5, CASC5, CENPM, CDC45, TACC3, MYLK, GINS2, CENPF, TGFBR2 | |||