Identification and Functional Enrichment Analysis of Differentially Expressed Genes in Osteoarthritis

Abstract Background Osteoarthritis (OA) is a chronic, progressive, inflammatory, degenerative disease, which has become an osteoarthropathy that seriously affects physical health and quality of life of elderly people. However, the etiology and pathogenesis of OA remains unclear. Therefore, the study purposed to utilize bioinformatics technology to perform identification and functional enrichment analysis of differentially expressed genes in osteoarthritis. Method The main methods of this study consist of access to microarray data (GSE82107 and GSE55235), identification of differently expressed genes (DEGs) by GEO2R between OA and normal synovium samples, enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) by Gene Set Enrichment Analysis (GSEA), construction and analysis of protein-protein interaction (PPI) network, significant module and hub genes. Result A total of 300 DEGs were identified, consisting of 64 up-regulated genes and 11 down-regulated genes in OA samples compared to normal synovium tissues. Gene set enrichment analysis of DEGs provided a comprehensive overview of some major pathophysiological mechanisms in OA: cellular response to hydrogen peroxide, P53 signaling pathway and so on. The study also built the PPI network, and a total of 10 key genes were identified: CYR61, PENK, GOLM1, DUSP1, ATF3, STC2, FOSB, PRSS23, TF, and TNC. Conclusion DEGs exists between OA patients and normal cartilage tissue, which may be involved in the related mechanism of OA development, especially cellular response to hydrogen peroxide and CYR61.