Journal of Shanghai Jiao Tong University (Medical Science) >

2021 , Vol. 41 >Issue 6: 749 - 755

DOI: https://doi.org/10.3969/j.issn.1674-8115.2021.06.007

Basic research

Screening of key genes and pathways involved in lupus nephritis based on GEO database

  • Yin LIU ,
  • Tao YANG ,
  • Yu-sai XIE ,
  • Yu-zhu WANG
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  • 1.Department of Nephrology, Beijing Haidian Hospital, Beijing 100080, China
    2.Department of Pathology, College of Basic Medical Sciences, China Medical University, Shenyang 110112, China

Online published: 2021-06-29

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Abstract

Objective

·To identify the differentially expressed genes and pathways involved in lupus nephritis (LN) using bioinformatics analysis.

Methods

·The matrix data of GSE32591 dataset was downloaded from the GEO database, and the limma package of R software was applied to standardize and screen the differentially expressed genes. The volcano map and heatmap of the differentially expressed genes were drawn by ggpubr and pheatmap packages. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes were performed using DAVID online database, and bar plot and bubble chart were drawn using R software ggplot package. STRING database and Cytoscape software were used to construct protein interaction networks of differentially expressed genes, and MCODE and cytohubba plug-ins were used to screen out the most significant modules and key genes involved in lupus nephritis. GSE99339 dataset was used to verify the differential expression of hub genes.

Results

·The GSE32591 data set was analyzed through the limma package, and 367 differentially expressed genes were obtained, including 253 up-regulated genes and 114 down-regulated genes. GO analysis and KEGG pathway enrichment analysis showed that differentially expressed genes were significantly enriched in virus defense response, cytoplasmic matrix, influenza A, tuberculosis, EB virus infection, complement pathway, etc. A protein interaction network of differentially expressed genes was constructed by STRING and Cytoscape, and 10 pivotal genes related to LN were identified. The hub genes are significantly differentially expressed in the GSE99339 validation dataset.

Conclusion

·The 367 differentially expressed genes and 10 hub genes are potential biomarkers of LN.

Key words： GEO database; lupus nephritis; systemic lupus erythematosus; bioinformatics; differentially expressed genes

Cite this article

Yin LIU , Tao YANG , Yu-sai XIE , Yu-zhu WANG . Screening of key genes and pathways involved in lupus nephritis based on GEO database[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2021 , 41(6) : 749 -755 . DOI: 10.3969/j.issn.1674-8115.2021.06.007

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