Prognostic genes of breast cancer revealed by gene co-expression network analysis

Oncology Letters
Huijie ShiMin Zheng

Abstract

The aim of the present study was to identify genes that may serve as markers for breast cancer prognosis by constructing a gene co-expression network and mining modules associated with survival. Two gene expression datasets of breast cancer were downloaded from ArrayExpress and genes from these datasets with a coefficient of variation >0.5 were selected and underwent functional enrichment analysis with the Database for Annotation, Visualization and Integration Discovery. Gene co-expression networks were constructed with the WGCNA package in R. Modules were identified from the network via cluster analysis. Cox regression was conducted to analyze survival rates. A total of 2,669 genes were selected, and functional enrichment analysis of them revealed that they were mainly associated with the immune response, cell proliferation, cell differentiation and cell adhesion. Seven modules were identified from the gene co-expression network, one of which was found to be significantly associated with patient survival time. Expression status of 144 genes from this module was used to cluster patient samples into two groups, with a significant difference in survival time revealed between these groups. These genes were involved in the cell cyc...Continue Reading

References

Dec 6, 1996·Science·K Nasmyth
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Feb 15, 2008·Cancer Science·Shin TakahashiChikashi Ishioka
Aug 5, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Shih-Yeh LinHey-Chi Hsu
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Jun 11, 2009·British Journal of Cancer·D LoussouarnP Jézéquel
Jan 14, 2010·Molecular Cancer Research : MCR·Jimmy M-M KwokEric W-F Lam
Apr 21, 2011·British Journal of Cancer·A Brüning-RichardsonS M Bell
May 12, 2011·JAMA : the Journal of the American Medical Association·Christos HatzisW Fraser Symmans
Jul 6, 2011·Breast Cancer Research and Treatment·Michelle D HolmesRulla M Tamimi
Nov 8, 2011·Annals of Oncology : Official Journal of the European Society for Medical Oncology·A PsyrriG Fountzilas
Feb 11, 2012·Molecular Biology of the Cell·Sanjay ShresthaCharles B Shuster
Jul 7, 2012·Future Oncology·Masoud H ManjiliXiang-Yang Wang
Feb 1, 2013·Oncology·Konstantinos KontzoglouMichael Stamatakos
Dec 10, 2013·The Journal of Clinical Investigation·Atsushi TerunumaStefan Ambs
Feb 14, 2014·Cancer Biology & Therapy·Shweta KotianJeffrey D Parvin
Nov 8, 2014·Molecules and Cells·Hui WangJingting Jiang
Apr 29, 2015·Oncogene·J JefferyK K Khanna
Jun 3, 2015·Breast Cancer Research and Treatment·Lei ZhangHuiqing Cao

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Datasets Mentioned

BETA
GSE2034
GSE25066
GPL96

Software Mentioned

rma
WGCNA
affy
DAVID
R

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