title: Identifying genes related with rheumatoid arthritis via system biology analysis.
abstract: Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease that mainly attacks synovial joints. However, the underlying systematic relationship among different genes and biological processes involved in the pathogenesis are still unclear. By analyzing and comparing the transcriptional profiles from RA, OA (osteoarthritis) patients as well as ND (normal donors) with bioinformatics methods, we tend to uncover the potential molecular networks and critical genes which play important roles in RA and OA development. Initially, hierarchical clustering was performed to classify the overall transcriptional profiles. Differentially expressed genes (DEGs) between ND and RA and OA patients were identified. Furthermore, PPI networks were constructed, functional modules were extracted, and functional annotation was also applied. Our functional analysis identifies 22 biological processes and 2 KEGG pathways enriched in the commonly-regulated gene set. However, we found that number of set of genes differentially expressed genes only between RA and ND reaches up to 244, indicating this gene set may specifically accounts for processing to disease of RA. Additionally, 142 biological processes and 19 KEGG pathways are over-represented by these 244 genes. Meanwhile, although another 21 genes were differentially expressed only in OA and ND, no biological process nor pathway is over-represented by them.
authors.affiliation: Department of Joint Surgery, affiliated Hospital of Binzhou Medical College, No. 661 Huanghe Er Road, Binzhou City, Shandong Province 256603, China. Electronic address: liutaobzh@163.com.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: Department of Joint Surgery, affiliated Hospital of Binzhou Medical College, No. 661 Huanghe Er Road, Binzhou City, Shandong Province 256603, China. Electronic address: linxmbzh@126.com.
authors.forename: Xinmei
authors.initials: X
authors.lastname: Lin
authors.affiliation: Department of Orthopaedics in Binzhou People Hospital, No. 515 Huanghe Qi Road, Binzhou City, Shandong Province 256603, China. Electronic address: yuhjbzh@163.com.
authors.forename: Hongjian
authors.initials: H
authors.lastname: Yu
mesh_terms: D001172:Arthritis, Rheumatoid / Q000235:genetics*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D006801:Humans; D008957:Models, Genetic; D060066:Protein Interaction Maps / Q000235:genetics; D015398:Signal Transduction / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
keywords: Differentially expressed genes; Molecular network; Related gene; Rheumatoid arthritis; Transcriptional profiles