title: Genes relevant with osteoarthritis by comparison gene expression profiles of synovial membrane of osteoarthritis patients at different stages.
abstract: BACKGROUND
  This study aimed to identify biological markers about osteoarthritis (OA) which is a polygenic disease by investigating the gene expression profiles of the synovium samples from early-stage and end-stage OA patients for the diagnosis and treatment of OA.
  
  
  METHODS
  The gene expression profile of GSE32317 was downloaded from Gene Expression Omnibus (GEO) database, including 10 samples from early-stage OA patients and 9 samples from end-stage OA patients. The differentially expressed genes (DEGs) were identified by Significance Analysis of Microarrays. The co-expression network of DEGs was constructed by Pearson correlation test. Then, modules in the constructed co-expression network were selected by MCODE Plugin. What's more, EASE (Expression Analysis Systematic Explorer) was used to define the significant functions and pathways in the identified modules.
  
  
  RESULTS
  Total 419 DEGs were identified, among which 112 were up-regulated and 307 down-regulated. We selected 7 statistically significant modules with gene number above 10 and phenotypic correlation test of modules showed that all the modules had significant correlation with OA (p < 0.05). The genes of module 1, module 2 and module 7 were significantly related to immune system functions, protein glycosylation functions, bone, chondrocytes and cartilage functions, respectively. The most significant pathway in module 3 and module 5 was Wnt signal pathway, and in module 4 was Toll-like receptor signal pathway.
  
  
  CONCLUSIONS
  DEGs related to immune response, cartilage development, protein glycosylation, muscle development, and DEGs participated in the Wnt signaling pathway and Toll-like receptor (TLR) signaling pathway might be the potential target genes for the OA treatment.
authors.affiliation: Department of Orthopedic Surgery, Shanghai First People's Hospital, Shanghai Jiao Tong University, Shanghai, China. chengqingyichqy@hotmail.com.
authors.forename: C-H
authors.initials: CH
authors.lastname: Ma
authors.forename: Q
authors.initials: Q
authors.lastname: Lv
authors.forename: Y
authors.initials: Y
authors.lastname: Cao
authors.forename: Q
authors.initials: Q
authors.lastname: Wang
authors.forename: X-K
authors.initials: XK
authors.lastname: Zhou
authors.forename: B-W
authors.initials: BW
authors.lastname: Ye
authors.forename: C-Q
authors.initials: CQ
authors.lastname: Yi
mesh_terms: D018450:Disease Progression; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D006801:Humans; D046228:Microarray Analysis; D005810:Multigene Family; D020370:Osteoarthritis, Knee / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D013583:Synovial Membrane / Q000378:metabolism* / Q000473:pathology; D059467:Transcriptome