Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis

BMC Microbiology

Jia-xin Li¹  Qiu-ying Li²  Xun-jie Cao²  Zi-yuan Yu²  Ji-chun Chen²  Xu-guang Guo³  Yuan-yi Huang⁴  Ya-ping Li⁵  Min Lin⁶ 

[1] Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, 510150, Guangzhou, China;Department of Clinical Medicine, The First Clinical School of Guangzhou Medical University, 511436, Guangzhou, China;Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, 510150, Guangzhou, China;Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, 511436, Guangzhou, China;Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, 510150, Guangzhou, China;Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 510150, Guangzhou, China;Department of Clinical Medicine, The First Clinical School of Guangzhou Medical University, 511436, Guangzhou, China;Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, 511436, Guangzhou, China;Department of Traditional Chinese and Western Clinical Medicine, The Traditional Chinese and Western Clinical School of Guangzhou Medical University, 511436, Guangzhou, China;

关键词: Staphylococcus aureus;    Weighted gene co-expression network analysis;    Mitophagy;    Bioinformatic analysis;   

DOI  :  10.1186/s12866-021-02392-y

来源: Springer

【 摘 要 】

IntroductionStaphylococcus aureus is a gram-positive bacterium that causes serious infection. With the increasing resistance of bacteria to current antibiotics, it is necessary to learn more about the molecular mechanism and cellular pathways involved in the Staphylococcus aureus infection.MethodsWe downloaded the GSE33341 dataset from the GEO database and applied the weighted gene co-expression network analysis (WGCNA), from which we obtained some critical modules. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were applied to illustrate the biological functions of genes in these modules. We constructed the protein-protein interaction (PPI) network by Cytoscape and selected five candidate hub genes. Five potential hub genes were validated in GSE30119 by GraphPad Prism 8.0. The diagnostic values of these genes were calculated and present in the ROC curve based on the GSE13670 dataset. Their gene functions were analyzed by Gene Set Enrichment Analysis (GSEA).ResultsA co-expression network was built with 5000 genes divided into 11 modules. The genes in green and turquoise modules demonstrated a high correlation. According to the KEGG and GO analyses, genes in the green module were closely related to ubiquitination and autophagy. Subsequently, we picked out the top five hub genes in the green module. And UBB was determined as the hub gene in the GSE30119 dataset. The expression level of UBB, ASB, and MKRN1 could significantly differentiate between Staphylococcus aureus infection and healthy controls based on the ROC curve. The GSEA analysis indicated that lower expression levels of UBB were associated with the P53 signal pathway.ConclusionsWe identified some hub genes and significant signal enrichment pathways in Staphylococcus aureus infection via bioinformatics analysis, which may facilitate the development of potential clinical therapeutic strategies.

【 授权许可】

CC BY