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Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis

  • Authors:
    • Xiangxiang Sun
    • Honghao Duan
    • Lin Xiao
    • Shuxin Yao
    • Qiang He
    • Xinlin Chen
    • Weijie Zhang
    • Jianbing Ma
  • View Affiliations / Copyright

    Affiliations: Department of Knee Surgery, Hong‑Hui Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi 710054, P.R. China
    Copyright: © Sun et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 18
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    Published online on: November 5, 2020
       https://doi.org/10.3892/etm.2020.9450
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Abstract

The present study aimed to identify key genes involved in osteoarthritis (OA). Based on a bioinformatics analysis of five gene expression profiling datasets (GSE55457, GSE55235, GSE82107, GSE12021 and GSE1919), differentially expressed genes (DEGs) in OA were identified. Subsequently, a protein‑protein interaction (PPI) network was constructed and its topological structure was analyzed. In addition, key genes in OA were identified following a principal component analysis (PCA) based on the DEGs in the PPI network. Finally, the functions and pathways enriched by these key genes were also analyzed. The PPI network consisted of 241 nodes and 576 interactives, including a total of 171 upregulated DEGs [e.g., aspartylglucosaminidase (AGA), CD58 and CD86] and a total of 70 downregulated DEGs (e.g., acetyl‑CoA carboxylase β and dihydropyrimidine dehydrogenase). The PPI network complied with an attribute of scale‑free small‑world network. After PCA, 47 key genes were identified, including β‑1,4‑galactosyltransferase‑1 (B4GALT1), AGA, CD58, CD86, ezrin, and eukaryotic translation initiation factor 4 γ 1 (EIF4G1). Subsequently, the 47 key genes were identified to be enriched in 13 Gene Ontology (GO) terms and 2 Kyoto Encyclopedia of Genes and Genomes pathways, with the GO terms involving B4GALT1 including positive regulation of developmental processes, protein amino acid terminal glycosylation and protein amino acid terminal N‑glycosylation. In addition, B4GALT1 and EIF4G1 were confirmed to be downregulated in OA samples compared with healthy controls, but only EIF4G1 was determined to be significantly downregulated in OA samples, as determined via a meta‑analysis of the 5 abovementioned datasets. In conclusion, B4GALT1 and EIF4G1 were indicated to have significant roles in OA, and B4GALT1 may be involved in positive regulation of developmental processes, protein amino acid terminal glycosylation and protein amino acid terminal N‑glycosylation. The present study may enhance the current understanding of the molecular mechanisms of OA and provide novel therapeutic targets.
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Copy and paste a formatted citation
Spandidos Publications style
Sun X, Duan H, Xiao L, Yao S, He Q, Chen X, Zhang W and Ma J: Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis. Exp Ther Med 21: 18, 2021.
APA
Sun, X., Duan, H., Xiao, L., Yao, S., He, Q., Chen, X. ... Ma, J. (2021). Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis. Experimental and Therapeutic Medicine, 21, 18. https://doi.org/10.3892/etm.2020.9450
MLA
Sun, X., Duan, H., Xiao, L., Yao, S., He, Q., Chen, X., Zhang, W., Ma, J."Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis". Experimental and Therapeutic Medicine 21.1 (2021): 18.
Chicago
Sun, X., Duan, H., Xiao, L., Yao, S., He, Q., Chen, X., Zhang, W., Ma, J."Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis". Experimental and Therapeutic Medicine 21, no. 1 (2021): 18. https://doi.org/10.3892/etm.2020.9450
Copy and paste a formatted citation
x
Spandidos Publications style
Sun X, Duan H, Xiao L, Yao S, He Q, Chen X, Zhang W and Ma J: Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis. Exp Ther Med 21: 18, 2021.
APA
Sun, X., Duan, H., Xiao, L., Yao, S., He, Q., Chen, X. ... Ma, J. (2021). Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis. Experimental and Therapeutic Medicine, 21, 18. https://doi.org/10.3892/etm.2020.9450
MLA
Sun, X., Duan, H., Xiao, L., Yao, S., He, Q., Chen, X., Zhang, W., Ma, J."Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis". Experimental and Therapeutic Medicine 21.1 (2021): 18.
Chicago
Sun, X., Duan, H., Xiao, L., Yao, S., He, Q., Chen, X., Zhang, W., Ma, J."Identification of key genes in osteoarthritis using bioinformatics, principal component analysis and meta‑analysis". Experimental and Therapeutic Medicine 21, no. 1 (2021): 18. https://doi.org/10.3892/etm.2020.9450
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