Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis

• DOI: 10.7717/peerj.6425
• Publication Date: 2019-02-25T03:35:57Z
• Authors: Yang Fang; Pingping Wang; Lin Xia; Suwen Bai; Yonggang Shen; Qing Li; Yang Wang; Jinhang Zhu; Juan Du; Bing Shen
• Keywords: KEGG; Interaction network

The elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, pathogenesis OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes pathways determine underlying molecular mechanisms susceptibility-related for inheritance.Gene expression microarray data, mRNA profile whole genome 5hmC dataset obtained from Gene Expression Omnibus repository. Differentially with abnormal hydroxymethylation identified by MATCH function. ontology Kyoto Encyclopedia Genes Genomes (KEGG) pathway enrichment OA performed using Metascape KOBAS online tool, respectively. protein-protein interaction network was built STRING visualized Cytoscape, modular analysis Molecular Complex Detection app.In total, 104 hyperhydroxymethylated highly 14 hypohydroxymethylated low identified. indicated that biological functions included skeletal system ossification, bone development; KEGG showed protein digestion absorption, extracellular matrix-receptor interaction, focal adhesion. top 10 hub COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, COL24A1. All aforementioned results are consistent changes observed OA.After bioinformatics analysis, we found useful biomarkers provide more accurate diagnoses target treatment