title: Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease.
abstract: BACKGROUND
  The analysis of the potential molecule targets of coronary artery disease (CAD) is critical for understanding the molecular mechanisms of disease. However, studies of global microarray gene co-expression analysis of CAD still remain limited.
  
  
  METHODS
  Microarray data of CAD (GSE23561) were downloaded from Gene Expression Omnibus, including peripheral blood samples from CAD patients (n = 6) and controls (n = 9). Limma package in R was used to identify the differentially expressed genes (DEGs) between CAD and control samples. Using weighted gene co-expression network analysis (WGCNA) package in R, WGCNA was performed to identify significant modules in the network. Then, functional and pathway enrichment analyses were conducted for genes in the most significant module using DAVID software. Moreover, hub genes in the module were analyzed by isubpathwayminer package in R and GenCLiP 2.0 tool to identify the significant sub-pathways.
  
  
  RESULTS
  Total 3711 DEGs and 21 modules for them were identified in CAD samples. The most significant module was associated with the pathways of hypertrophic cardiomyopathy and membrane related functions. In addition, the top 30 hub genes with high connectivity in the module were selected, and two genes (G6PD and S100A7) were taken as key molecules via sub-pathway screening and data mining.
  
  
  CONCLUSIONS
  A module associated with hypertrophic cardiomyopathy pathway was detected in CAD samples. G6PD and S100A7 were the potential targets in CAD. Our finding might provide novel insight into the underlying molecular mechanism of CAD.
authors.affiliation: Department of Cardiology, Harbin the second hospital, Harbin, Heilongjiang, 150056, China. JingLiujll@163.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Cardiology, First affiliated hospital of Harbin medical university, Harbin, Heilongjiang, 150036, China. lingjingljj@163.com.|Department of Cardiology, First Clinical College of Harbin Medical University, Harbin, Heilongjiang, 150001, China. lingjingljj@163.com.
authors.forename: Ling
authors.initials: L
authors.lastname: Jing
authors.affiliation: Emergency Internal Medicine, First affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150036, China. XilinTuxlt@163.com.
authors.forename: Xilin
authors.initials: X
authors.lastname: Tu
mesh_terms: D002312:Cardiomyopathy, Hypertrophic / Q000235:genetics; D016022:Case-Control Studies; D019295:Computational Biology; D003324:Coronary Artery Disease / Q000175:diagnosis / Q000235:genetics*; D057225:Data Mining; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D005954:Glucosephosphate Dehydrogenase / Q000235:genetics; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D012333:RNA, Messenger / Q000235:genetics; D000075023:S100 Calcium Binding Protein A7; D009418:S100 Proteins / Q000235:genetics
chemical_list: D005819:Genetic Markers; D012333:RNA, Messenger; D000075023:S100 Calcium Binding Protein A7; D009418:S100 Proteins; C089242:S100A7 protein, human; D005954:Glucosephosphate Dehydrogenase