Bioinformatics Analyses of Regulatory Network of Biomarkers in Chondrocytes from Patients with Osteoarthritis

Abstract

Abstract This study aimed to explore the biomarkers associated with osteoarthritis (OA). Gene expression profile GSE16464 was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in chondrocytes between OA patients and normal donors were analyzed, which were then subjected to Gene Ontology (GO) and pathway enrichment analyses, followed by microRNA (miRNA) and transcription factor (TF) prediction, and regulatory network construction. Finally, the copy number variants (CNVs) of target genes were searched. Total 79 up- and 147 down-regulated DEGs were identified. Nine GO terms were obtained and the biological process (BP) term related to neuron differentiation was enriched by 13 DEGs, such as GNAO1, POU3F4 andRPS27A. Pathway of regulation of actin cytoskeleton was enriched by six DEGs such as FGF18. Six miRNAs such as miRNA-524 and seven TFs, such as FOXO4 were detected. In the regulatory network, GNAO1, POU3F4 and RPS27A were key target genes and their CNVs were identified. Pathway of regulation of actin cytoskeleton and BP related to neuron differentiation may play important roles in OA progression. DEGs of FGF18, GNAO1 and POU3F4 as well as their regulatory factors such as FOXO4 and miRNA-524 may be potential biomarkers associated with OA.

Keywords

• osteoarthritis
• differentially expressed genes
• functional enrichment analysis
• microRNA
• transcription factor
• regulatory network