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Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy

  • Authors:
    • Dongmei Zhang
    • Yiling Cao
    • Yongdi Zuo
    • Zheng Wang
    • Xuhua Mi
    • Wanxin Tang
  • View Affiliations / Copyright

    Affiliations: Department of Nephrology, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, P.R. China
    Copyright: © Zhang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1235-1245
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    Published online on: June 18, 2019
       https://doi.org/10.3892/etm.2019.7686
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Abstract

Immunoglobulin A (IgA) nephropathy (IgAN) is the most common glomerular disease. The major pathological changes associated with it affect cell proliferation, fibrosis, apoptosis, inflammation and extracellular matrix (ECM) organization. However, the molecular events underlying IgAN remain to be fully elucidated. In the present study, an integrated bioinformatics analysis was applied to further explore novel potential gene targets for IgAN. The mRNA expression profile datasets GSE93798 and GSE37460 were downloaded from the Gene Expression Omnibus database. After data preprocessing, differentially expressed genes (DEGs) were identified. Gene Ontology (GO) enrichment analysis of DEGs was performed. Protein‑protein interaction (PPI) networks of the DEGs were built with the STRING online search tool and visualized by using Cytoscape, and hub genes were identified through the degree of connectivity in the PPI. The hub genes were subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis, and co‑expression analysis was performed. A total of 298 DEGs between IgAN and control groups were identified, and 148 and 150 of these DEGs were upregulated and downregulated, respectively. The DEGs were enriched in distinct GO terms for Biological Process, including cell growth, epithelial cell proliferation, ERK1 and ERK2 cascades, regulation of apoptotic signaling pathway and ECM organization. The top 10 hub genes were then screened from the PPI network by Cytoscape. As novel hub genes, Fos proto‑oncogene, AP‑1 transcription factor subunit and early growth response 1 were determined to be closely associated with apoptosis and cell proliferation in IgAN. Tumor protein 53, integrin subunit β2 and fibronectin 1 may also be involved in the occurrence and development of IgAN. Co‑expression analysis suggested that these hub genes were closely linked with each other. In conclusion, the present integrated bioinformatics analysis provided novel insight into the molecular events and novel candidate gene targets of IgAN.
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Copy and paste a formatted citation
Spandidos Publications style
Zhang D, Cao Y, Zuo Y, Wang Z, Mi X and Tang W: Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy. Exp Ther Med 18: 1235-1245, 2019.
APA
Zhang, D., Cao, Y., Zuo, Y., Wang, Z., Mi, X., & Tang, W. (2019). Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy. Experimental and Therapeutic Medicine, 18, 1235-1245. https://doi.org/10.3892/etm.2019.7686
MLA
Zhang, D., Cao, Y., Zuo, Y., Wang, Z., Mi, X., Tang, W."Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy". Experimental and Therapeutic Medicine 18.2 (2019): 1235-1245.
Chicago
Zhang, D., Cao, Y., Zuo, Y., Wang, Z., Mi, X., Tang, W."Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy". Experimental and Therapeutic Medicine 18, no. 2 (2019): 1235-1245. https://doi.org/10.3892/etm.2019.7686
Copy and paste a formatted citation
x
Spandidos Publications style
Zhang D, Cao Y, Zuo Y, Wang Z, Mi X and Tang W: Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy. Exp Ther Med 18: 1235-1245, 2019.
APA
Zhang, D., Cao, Y., Zuo, Y., Wang, Z., Mi, X., & Tang, W. (2019). Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy. Experimental and Therapeutic Medicine, 18, 1235-1245. https://doi.org/10.3892/etm.2019.7686
MLA
Zhang, D., Cao, Y., Zuo, Y., Wang, Z., Mi, X., Tang, W."Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy". Experimental and Therapeutic Medicine 18.2 (2019): 1235-1245.
Chicago
Zhang, D., Cao, Y., Zuo, Y., Wang, Z., Mi, X., Tang, W."Integrated bioinformatics analysis reveals novel hub genes closely associated with pathological mechanisms of immunoglobulin A nephropathy". Experimental and Therapeutic Medicine 18, no. 2 (2019): 1235-1245. https://doi.org/10.3892/etm.2019.7686
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