Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia.

Abstract

Brain ischemia leads to energy depletion, mitochondrial dysfunction and neuronal cell death. The present study was designed to identify key genes and pathways associated with brain ischemia. The gene expression profile GSE52001, including 3 normal brain samples and 3 cerebral ischemia samples, was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified using the limma package. Then functional and pathway enrichment analyses were performed by the MATHT tool. Protein-protein interaction (PPI) network, module selection and microRNA (miRNA)-target gene network were constructed utilizing Cytoscape software. A total of 488 DEGs were identified (including 281 upregulated and 207 downregulated genes). In the PPI network, Rac family small GTPase 2 (RAC2) had higher degrees. RAC2 was significantly enriched in the FcγR-mediated phagocytosis pathway. miR-29A/B/C had a higher degree in the miRNA-target gene network. Insulin like growth factor 1 (Igf1) was identified as the target gene for miR-29A/B/C. RAC2 may function in brain ischemia through mediating the FcγR-mediated phagocytosis pathway. Meanwhile, miR-29A/B/C and their targets gene Igf1 may serve important roles in the development and progression of brain ischemia.