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Article

Differential co-expression analysis of rheumatoid arthritis with microarray data

  • Authors:
    • Kunpeng Wang
    • Liqiang Zhao
    • Xuefeng Liu
    • Zhenyong Hao
    • Yong Zhou
    • Chuandong Yang
    • Hongqiang Li
  • View Affiliations / Copyright

    Affiliations: Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China, Department of Orthopedics, The Harbin Fifth Hospital, Harbin, Heilongjiang 150001, P.R. China
  • Pages: 2421-2426
    |
    Published online on: August 14, 2014
       https://doi.org/10.3892/mmr.2014.2491
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Abstract

The aim of the present study was to investigate the underlying molecular mechanisms of rheumatoid arthritis (RA) using microarray expression profiles from osteoarthritis and RA patients, to improve diagnosis and treatment strategies for the condition. The gene expression profile of GSE27390 was downloaded from Gene Expression Omnibus, including 19 samples from patients with RA (n=9) or osteoarthritis (n=10). Firstly, the differentially expressed genes (DEGs) were obtained with the thresholds of |logFC|>1.0 and P<0.05, using the t‑test method in LIMMA package. Then, differentially co-expressed genes (DCGs) and differentially co-expressed links (DCLs) were screened with q<0.25 by the differential coexpression analysis and differential regulation analysis of gene expression microarray data package. Secondly, pathway enrichment analysis for DCGs was performed by the Database for Annotation, Visualization and Integrated Discovery and the DCLs associated with RA were selected by comparing the obtained DCLs with known transcription factor (TF)-targets in the TRANSFAC database. Finally, the obtained TFs were mapped to the known TF-targets to construct the network using cytoscape software. A total of 1755 DEGs, 457 DCGs and 101988 DCLs were achieved and there were 20 TFs in the obtained six TF-target relations (STAT3-TNF, PBX1‑PLAU, SOCS3-STAT3, GATA1-ETS2, ETS1-ICAM4 and CEBPE‑GATA1) and 457 DCGs. A number of TF-target relations in the constructed network were not within DCLs when the TF and target gene were DCGs. The identified TFs may have an important role in the pathogenesis of RA and have the potential to be used as biomarkers for the development of novel diagnostic and therapeutic strategies for RA.
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Copy and paste a formatted citation
Spandidos Publications style
Wang K, Zhao L, Liu X, Hao Z, Zhou Y, Yang C and Li H: Differential co-expression analysis of rheumatoid arthritis with microarray data. Mol Med Rep 10: 2421-2426, 2014.
APA
Wang, K., Zhao, L., Liu, X., Hao, Z., Zhou, Y., Yang, C., & Li, H. (2014). Differential co-expression analysis of rheumatoid arthritis with microarray data. Molecular Medicine Reports, 10, 2421-2426. https://doi.org/10.3892/mmr.2014.2491
MLA
Wang, K., Zhao, L., Liu, X., Hao, Z., Zhou, Y., Yang, C., Li, H."Differential co-expression analysis of rheumatoid arthritis with microarray data". Molecular Medicine Reports 10.5 (2014): 2421-2426.
Chicago
Wang, K., Zhao, L., Liu, X., Hao, Z., Zhou, Y., Yang, C., Li, H."Differential co-expression analysis of rheumatoid arthritis with microarray data". Molecular Medicine Reports 10, no. 5 (2014): 2421-2426. https://doi.org/10.3892/mmr.2014.2491
Copy and paste a formatted citation
x
Spandidos Publications style
Wang K, Zhao L, Liu X, Hao Z, Zhou Y, Yang C and Li H: Differential co-expression analysis of rheumatoid arthritis with microarray data. Mol Med Rep 10: 2421-2426, 2014.
APA
Wang, K., Zhao, L., Liu, X., Hao, Z., Zhou, Y., Yang, C., & Li, H. (2014). Differential co-expression analysis of rheumatoid arthritis with microarray data. Molecular Medicine Reports, 10, 2421-2426. https://doi.org/10.3892/mmr.2014.2491
MLA
Wang, K., Zhao, L., Liu, X., Hao, Z., Zhou, Y., Yang, C., Li, H."Differential co-expression analysis of rheumatoid arthritis with microarray data". Molecular Medicine Reports 10.5 (2014): 2421-2426.
Chicago
Wang, K., Zhao, L., Liu, X., Hao, Z., Zhou, Y., Yang, C., Li, H."Differential co-expression analysis of rheumatoid arthritis with microarray data". Molecular Medicine Reports 10, no. 5 (2014): 2421-2426. https://doi.org/10.3892/mmr.2014.2491
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