Identification by microarray technology of key genes involved in the progression of carotid atherosclerotic plaque

A comparative analysis of gene expression profiles between early and advanced carotid atherosclerotic plaque was performed to identify key genes and pathways involved in the progression of carotid atherosclerotic plaque. Gene expression data set GSE28829 was downloaded from Gene Expression Omnibus, including 13 early and 16 advanced atherosclerotic plaque samples from human carotid. Differentially expressed genes (DEGs) were identified using the package limma of R. Principal component analysis was carried out for the DEGs with package rgl of R. A gene coexpression network was constructed with information from COXPRESdb and then visualized with Cytoscape. Functional enrichment analysis was performed with DAVID and pathway enrichment analysis was done with KEGG. A total of 319 DEGs were identified in the advanced atherosclerotic plaque samples compared with early atherosclerotic plaque samples, including 267 up-regulated genes and 52 down-regulated genes. In the gene coexpression network, TYRO protein tyrosine kinase binding protein was the hub gene with a degree of 23. Functional enrichment analysis and pathway enrichment analysis suggested that the immune response played a critical role in the progression of carotid atherosclerotic plaque. A number of key genes were revealed in carotid atherosclerotic plaque, and are potential biomarkers for diagnosis or treatment. These findings may also guide future research to better decipher the progression of atherosclerosis.