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Table 3 Subnetwork enrichment.

From: Prediction of epigenetically regulated genes in breast cancer cell lines

Common regulator Predicted biomarkers p-value
GF S100A6,CD44,CDKN2A,CTGF,ESR1,IGFBP5,TFF1,GSTP1 2.86E-07
  IGFBP2,GJA1,WNT5A,NUPR1,S100A2  
Jun/Fos CD44,CYP1B1,CDKN2A,CTGF,ESR1,IGFBP5,TFF1,GSTP1 1.68E-06
  GJA1,PTN,COL1A2,S100A2,IFI16  
EGF CD44,CTGF,ESR1,IGFBP5,TFF1,KRT18,INHBA,IGFBP2 4.09E-06
  GJA1,PTN,COL1A2,S100A2  
TP53 CD44,CDKN2A,ESR1,SEMA3F,ANXA1,TFAP2A,COL1A2,LITAF 8.52E-06
  S100A2,TOP2A,FDXR,IFI16  
BMP2 CTGF,IGFBP5,INHBA,GJA1,WNT5A,CRABP2,COL1A2,ZIC1 8.56E-06
MAPK GATA3,CD44,CDKN2A,CTGF,ESR1,IGFBP5,MAFB,TFF1 9.57E-06
  IGFBP2,GJA1,TFAP2A,COL1A2  
PKA CYP1B1, CTGF, ESR1, IGFBP5, TFF1, KRT18, INHBA, IGFBP2 1.04E-05
  GJA1, TFAP2A  
TNF S100A6,CD44,CYP1B1,CTGF,ESR1,IGFBP5,TFF1,GSTP1 1.71E-05
  INHBA,GJA1,PTN,IGFBP7,TFAP2A,COL1A2,MX1  
SRC CD44,CTGF,ESR1,TFF1,KRT18,IGFBP2,COL1A2 2.30E-05
TGF family GATA3,CD44,CDKN2A,CTGF,IGFBP5,INHBA,GJA1,IGFBP7 2.89E-05
  CRABP2,COL1A2,VAV3  
  1. Top 10 lowest p-valued pathways identified by subnetwork enrichment analysis of the predicted 58 genes through Pathway Studio (see complete list in Additional file 2). Common regulator, genes involved and respective p-values are shown. The occurrence of multiple predicted markers within the same pathway suggests that epigenetic regulation of individual genes occurs in a coordinated fashion and through common regulators.