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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.
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BMC Bioinformatics

ISSN: 1471-2105

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