title: Identification of genes associated with osteoarthritis by microarray analysis.
abstract: The aim of the present study was to investigate the mechanisms of osteoarthritis (OA). Raw microarray data (GSE51588) were downloaded from Gene Expression Omnibus, including samples from OA (n=20) and non‑OA (n=5) knee lateral and medial tibial plateaus. Differentially expressed genes (DEGs) were identified using Student's t‑test. Functional and pathway enrichment analyses were performed for the upregulated and downregulated DEGs. A protein‑protein interaction network (PPI) was constructed according to the Search Tool for the Retrieval of Interacting Genes/Proteins database, and module analysis of the PPI network was performed using CFinder. The protein domain enrichment analysis for genes in modules was performed using the INTERPRO database. A total of 869 upregulated and 508 downregulated DEGs were identified. The enriched pathways of downregulated and upregulated DEGs were predominantly associated with the cell cycle (BUB1, BUB1B, CCNA2, CCNB1 and CCNE1), and extracellular matrix (ECM)‑receptor interaction (CD36, COL11A2, COL1A1, COL2A1 and COL3A1). Functional enrichment analysis of the DEGs demonstrated that FGF19, KIF11 and KIF2C were involved in the response to stress and that ACAN, ADAMTS10 and BGN were associated with proteinaceous ECM. The top protein domain was IPR001752: Kinesin motor region involving three genes (KIF2C, KIF11 and KIF20A). The identified DEGs, including KIF2C, KIF11 and KIF20A, may be significant in the pathogenesis of OA.
authors.affiliation: Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Sun
authors.affiliation: Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China.
authors.forename: Bingshan
authors.initials: B
authors.lastname: Yan
authors.affiliation: Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China.
authors.forename: Wangping
authors.initials: W
authors.lastname: Yin
authors.affiliation: Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China.
authors.forename: Xinchao
authors.initials: X
authors.lastname: Zhang
mesh_terms: D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D006801:Humans; D010003:Osteoarthritis / Q000235:genetics* / Q000378:metabolism; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps