Microarray analysis of hub genes and pathways in damaged cartilage tissues of knee

Abstract

The aim of this study was to identify genes and functional pathways associated with damaged cartilage tissues of knee using microarray analysis. The gene expression profile GSE129147 including including 10 knee cartilage tissues from damaged side and 10 knee nonweightbearing healthy cartilage was downloaded and bioinformatics analysis was made. A total of 182 differentially-expressed genes including 123 up-regulated and 59 down-regulated genes were identified from the GSE129147 dataset. Gene ontology and pathway enrichment analysis confirmed that extracellular matrix organization, collagen catabolic process, antigen processing and presentation of peptide or polysaccharide antigen, and endocytic vesicle membrane were strongly associated with cartilage injury. Furthermore, 10 hub differentially-expressed genes with a higher connectivity degree in protein protein interactions network were found such as POSTN, FBN1, LOX, insulin-like growth factor binding proteins3, C3AR1, MMP2, ITGAM, CDKN2A, COL1A1, COL5A1. These hub genes and pathways provide a new perspective for revealing the potential pathological mechanisms and therapy strategy of cartilage injury. Abbreviations: BPs = biological processes, DEGs = differentially-expressed genes, FBN1 = fibrillin-1, GO = gene ontology, IGFBP = insulin-like growth factor binding protein, IGF-I = Insulin-like growth factor-I, LOX = lysyl oxidase, MCODE = molecular complex detection, MHC = major histocompatibility complex, PPI = protein protein interactions.