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

Abstract Introduction Staphylococcus 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...

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Autores principales:	Jia-xin Li, Xun-jie Cao, Yuan-yi Huang, Ya-ping Li, Zi-yuan Yu, Min Lin, Qiu-ying Li, Ji-chun Chen, Xu-guang Guo
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Staphylococcus aureus Weighted gene co-expression network analysis Mitophagy Bioinformatic analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a0f1dcf82b4241bda633c76821ff2ec3
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spelling	oai:doaj.org-article:a0f1dcf82b4241bda633c76821ff2ec32021-12-05T12:06:12ZInvestigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis10.1186/s12866-021-02392-y1471-2180https://doaj.org/article/a0f1dcf82b4241bda633c76821ff2ec32021-12-01T00:00:00Zhttps://doi.org/10.1186/s12866-021-02392-yhttps://doaj.org/toc/1471-2180Abstract Introduction Staphylococcus 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. Methods We 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). Results A 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. Conclusions We 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.Jia-xin LiXun-jie CaoYuan-yi HuangYa-ping LiZi-yuan YuMin LinQiu-ying LiJi-chun ChenXu-guang GuoBMCarticleStaphylococcus aureusWeighted gene co-expression network analysisMitophagyBioinformatic analysisMicrobiologyQR1-502ENBMC Microbiology, Vol 21, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Staphylococcus aureus Weighted gene co-expression network analysis Mitophagy Bioinformatic analysis Microbiology QR1-502
spellingShingle	Staphylococcus aureus Weighted gene co-expression network analysis Mitophagy Bioinformatic analysis Microbiology QR1-502 Jia-xin Li Xun-jie Cao Yuan-yi Huang Ya-ping Li Zi-yuan Yu Min Lin Qiu-ying Li Ji-chun Chen Xu-guang Guo Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
description	Abstract Introduction Staphylococcus 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. Methods We 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). Results A 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. Conclusions We 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.
format	article
author	Jia-xin Li Xun-jie Cao Yuan-yi Huang Ya-ping Li Zi-yuan Yu Min Lin Qiu-ying Li Ji-chun Chen Xu-guang Guo
author_facet	Jia-xin Li Xun-jie Cao Yuan-yi Huang Ya-ping Li Zi-yuan Yu Min Lin Qiu-ying Li Ji-chun Chen Xu-guang Guo
author_sort	Jia-xin Li
title	Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
title_short	Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
title_full	Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
title_fullStr	Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
title_full_unstemmed	Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis
title_sort	investigation of hub gene associated with the infection of staphylococcus aureus via weighted gene co-expression network analysis
publisher	BMC
publishDate	2021
url	https://doaj.org/article/a0f1dcf82b4241bda633c76821ff2ec3
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Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis

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