Table 1 Key features of eight predominant gene co-expression modules extracted by WGCNA.
From: Epigenome erosion and SOX10 drive neural crest phenotypic mimicry in triple-negative breast cancer
Modules | Major functional ontologiesa | Signalling pathwaysa/intrinsic activatorsb | Size (no. genes) | Top ten hub genes (Highest kWithin; see Supplementary Table 5) | |
|---|---|---|---|---|---|
Tumour-centric | Blue | Mitotic instability | FOXM1, MYBL2 | 1239 | TPX2, BUB1, CEP55, HJURP, NCAPH, KIF4A, KIF2C, CCNB2, NCAPG, FOXM1 |
Green | Multipotency (SOXE) | Wnt signalling | 487 | ROPN1, SFRP1, FOXC1, RGMA, GABRP, CHST3, MAML2, APCN, ROPN1B, SOX10 | |
Brown | Primary cilium | ER, FOXA1 | 1008 | FOXA1, MLPH, ESR1, AGR3, XBP1, THSD4, GATA3, CA12, PRR15, ZMYND10 | |
Tumour-stromal | Magenta | ECM-1 (structural) | FBN1, RUNX2 | 186 | COL5A2, COL1A2, COL3A1, COL5A1, COL6A3, FAP, THBS2, COL1A1, LUM, VCAN |
Black | ECM2 (regulatory) | – | 207 | OLFML1, RECK, FSTL1, DCN, MSRB3, ECM2, CCDC80, TCF4, ZEB1, GLT8D2 | |
Red | Fatty acid metabolism | PPARγ | 274 | DIA1R, PDE2A, LHFP, LDB2, ARHGEF15, S1PR1, SDPR, EBF1, CD34, ERG | |
Tan | Type-I IFN response | STAT1, IRF9 | 33 | IFIT3, OAS2, CMPK2, IFI44L, IFI44, IFIT1, MX1, OASL, IFIT2, RSAD2 | |
Stromal | Yellow | Adaptive immunity (TILs) | CD40L, CD40, IFNγ, IRF1 | 712 | SASH3, IL2RG, CD53, PTPN7, CD48, CD2, CD3E, ARHGAP9, CD5, CD3D, SIT1, SH2D1A |
