Analysis of differentially expressed genes between rheumatoid arthritis and osteoarthritis based on the gene co-expression network.
The aim of the current study was to investigate disease-associated genes and related molecular mechanisms of osteoarthritis (OA) and rheumatoid arthritis (RA). Using GSE7669 datasets downloaded from Gene Expression Omnibus databases, the differentially expressed genes (DEGs) between RA and OA synovial fibroblasts (SFBs) (n=6 each) were screened. DEG-associated co-expression and topological properties were analyzed to determine the rank of disease-associated genes. Specifically, the fold change of differentially expressed genes, the clustering coefficient and the degree of differential gene co-expression were integrated to determine the disease-associated gene ranking. The underlying molecular mechanisms of these crucial disease-associated genes were investigated by gene ontology (GO) enrichment analysis. A total of 1313 DEGs, including 1068 upregulated genes and 245 downregulated genes were observed. The top 20 disease-associated genes were identified, including proteoglycan 4, inhibin β B, carboxypeptidase M, alcohol dehydrogenase 1C and integrin β2. The major GO biological processes of these top 20 disease-associated genes were highly involved in the immune system, such as responses to stimuli, immune responses and inflammatory responses. This large-scale gene expression study observed disease-associated genes and their associated GO function in RA and OA, which may provide opportunities for biomarker development and novel insights into the molecular mechanisms of these two diseases.
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Qing-You
QY
Lu
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Qing-Hui
QH
Han
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Xia
X
Li
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Zeng-Chun
ZC
Li
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Yu-Tao
YT
Pan
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Lin
L
Liu
Department of Trauma Surgery, East Hospital Affiliated to Tongji University, Shanghai 200120, P.R. China.
Qing-Ge
QG
Fu
D001172:Arthritis, Rheumatoid / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D016000:Cluster Analysis; D030541:Databases, Genetic; D015536:Down-Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010003:Osteoarthritis / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D013583:Synovial Membrane / Q000378:metabolism; D015854:Up-Regulation