Skip to main content

Table 3 Gene enrichment in the three subsets of CpGs exhibiting differential methylation between the LumA-M1 and LumA-M3 subgroups

From: Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups

 

(1)

 

(2)

 

(3)

 
 

Hyper-methylated CpGs

 

Negative: R < -0.2

 

Positive: R > 0.2

 
 

1000 CpGs, 483 genes

586 CpGs, 340 genes

212 CpGs, 125 genes

 

Term

P value

Term

P value

Term

P value

Gene Ontology

Anatomical structure development

6.1e-28

Developmental process

7.8e-06

Pattern specification process

1.1e-13

Developmental process

2.0e-25

Single organism signaling

2.4e-05

Regionalization

1.1e-12

Multicellular organismal process

9.6e-24

Signaling

1.8e-05

Anatomical structure development

2.2e-11

Single multicellular organism process

1.6e-22

Cellular developmental process

1.4e-05

Single organism developmental process

1.9e-11

Single organism signaling

1.7e-21

Single organism developmental process

2.3e-05

Anatomical structure morphogenesis

1.8e-11

Signaling

1.9e-21

Anatomical structure development

8.0e-05

Developmental process

1.7e-11

Cell-cell signaling

1.7e-21

Cell-cell signaling

1.8e-04

Embryonic morphogenesis

1.1e-10

Neuron differentiation

1.2e-20

Cell differentiation

2.2e-04

Cellular developmental process

1.8e-10

Single organism developmental process

1.4e-19

Synaptic transmission

4.4e-04

Organ development

5.3e-10

Regulation of transcription from RNA polymerase II promoter

1.2e-16

Anatomical structure morphogenesis

6.1e-04

Single multicellular organism process

5.6e-10

InterPro

Homeobox

3.6e-35

Homeobox

1.1e-04

Homeobox

2.1e-31

Tumor suppressor genes (TSGene 2.0)

AHRR, AKR1B1, BMP2, C2orf40, CDH4, CDO1, CDX2, CNTNAP2, CSMD1, DLK1, DSC3, EBF3, EDNRB, FAT4, FOXA2, FOXC1, GALR1, GREM1, GRIN2A, ID4, IRF4, IRX1, LHX4, MAL, MIR124-2, MIR124-3, MIR125B1, MIR129-2, MIR137, MIR9-3, ONECUT1, OPCML, PAX5, PAX6, PCDH8, PHOX2A, PRKCB, PROX1, PTGDR, RASL10B, SFRP1, SFRP2, SHISA3, SLIT2, SOX7, TBX5, UNC5D, ZIC1

1.5e-03

AKR1B1, ASCL1, BIN1, BMP4, CCDC67, CDK6, CDO1, EBF3, GSTP1, ID4, IRX1, L3MBTL4, LRRC4, MAP4K1, MME, NTRK3, PCDH10, PDLIM4, PROX1, PTGDR, RUNX3, SCGB3A1, SFRP1, SLC5A8, SLIT2, UBE2QL1, UNC5B, VIM, WT1

9.7e-02

AMH, GATA4, HOPX, HOXB13, LHX4, LHX6, MAP4K1, ONECUT1, PAX5, RASAL1, TBX5, TP73, WT1, ZIC1

5.5e-02

(48 genes)

(29 genes)

(14 genes)

Back to article page

Breast Cancer Research

ISSN: 1465-542X

Contact us