title: Genome-wide association studies and gene expression profiles of rheumatoid arthritis: An analysis.
abstract: OBJECTIVE
  The molecular mechanism of rheumatoid arthritis (RA) remains elusive. We conducted a protein-protein interaction network-based integrative analysis of genome-wide association studies (GWAS) and gene expression profiles of RA.
  
  
  METHODS
  We first performed a dense search of RA-associated gene modules by integrating a large GWAS meta-analysis dataset (containing 5539 RA patients and 20 169 healthy controls), protein interaction network and gene expression profiles of RA synovium and peripheral blood mononuclear cells (PBMCs). Gene ontology (GO) enrichment analysis was conducted by DAVID. The protein association networks of gene modules were generated by STRING.
  
  
  RESULTS
  For RA synovium, the top-ranked gene module is HLA-A, containing TAP2, HLA-A, HLA-C, TAPBP and LILRB1 genes. For RA PBMCs, the top-ranked gene module is GRB7, consisting of HLA-DRB5, HLA-DRA, GRB7, CD63 and KIT genes. Functional enrichment analysis identified three significant GO terms for RA synovium, including antigen processing and presentation of peptide antigen via major histocompatibility complex class I (false discovery rate (FDR) = 4.86 × 10 - 4), antigen processing and presentation of peptide antigen (FDR = 2.33 × 10 - 3) and eukaryotic translation initiation factor 4F complex (FDR = 2.52 × 10 - 2).
  
  
  CONCLUSIONS
  This study reported several RA-associated gene modules and their functional association networks.Cite this article: X. Xiao, J. Hao, Y. Wen, W. Wang, X. Guo, F. Zhang. Genome-wide association studies and gene expression profiles of rheumatoid arthritis: an analysis. Bone Joint Res 2016;5:314-319. DOI: 10.1302/2046-3758.57.2000502.
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China.
authors.forename: X
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China.
authors.forename: J
authors.initials: J
authors.lastname: Hao
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Wen
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China.
authors.forename: W
authors.initials: W
authors.lastname: Wang
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China.
authors.forename: X
authors.initials: X
authors.lastname: Guo
authors.affiliation: Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Yanta West Road 76, Xi'an, Shaanxi, China fzhxjtu@mail.xjtu.edu.cn.
authors.forename: F
authors.initials: F
authors.lastname: Zhang
keywords: Gene modules; Genome-wide association studies; Microarray; Protein interaction network; Rheumatoid arthritis