Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma

Abstract Background Asthma is a heterogeneous disease that can be divided into four inflammatory phenotypes: eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma (MGA), and paucigranulocytic asthma (PGA). While research has mainly focused on EA and NA, the understanding of P...

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Autores principales:	Min Li, Wenye Zhu, Chu Wang, Yuanyuan Zheng, Shibo Sun, Yan Fang, Zhuang Luo
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Paucigranulocytic asthma Immune status WGCNA Hub genes Diseases of the respiratory system RC705-779
Acceso en línea:	https://doaj.org/article/eb64ae82e5a643e38060f29d686dd583
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spelling	oai:doaj.org-article:eb64ae82e5a643e38060f29d686dd5832021-11-08T11:13:18ZWeighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma10.1186/s12890-021-01711-31471-2466https://doaj.org/article/eb64ae82e5a643e38060f29d686dd5832021-11-01T00:00:00Zhttps://doi.org/10.1186/s12890-021-01711-3https://doaj.org/toc/1471-2466Abstract Background Asthma is a heterogeneous disease that can be divided into four inflammatory phenotypes: eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma (MGA), and paucigranulocytic asthma (PGA). While research has mainly focused on EA and NA, the understanding of PGA is limited. In this study, we aimed to identify underlying mechanisms and hub genes of PGA. Methods Based on the dataset from Gene Expression Omnibus(GEO), weighted gene coexpression network analysis (WGCNA), differentially expressed genes (DEGs) analysis and protein–protein interaction (PPI) network analysis were conducted to construct a gene network and to identify key gene modules and hub genes. Functional enrichment analyses were performed to investigate the biological process, pathways and immune status of PGA. The hub genes were validated in a separate dataset. Results Compared to non-PGA, PGA had a different gene expression pattern, in which 449 genes were differentially expressed. One gene module significantly associated with PGA was identified. Intersection between the differentially expressed genes (DEGs) and the genes from the module that were most relevant to PGA were mainly enriched in inflammation and immune response regulation. The single sample Gene Set Enrichment Analysis (ssGSEA) suggested a decreased immune infiltration and function in PGA. Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268. Conclusions Our study characterized distinct gene expression patterns, biological processes and immune status of PGA and identified hub genes, which may improve the understanding of underlying mechanism and provide potential therapeutic targets for PGA.Min LiWenye ZhuChu WangYuanyuan ZhengShibo SunYan FangZhuang LuoBMCarticlePaucigranulocytic asthmaImmune statusWGCNAHub genesDiseases of the respiratory systemRC705-779ENBMC Pulmonary Medicine, Vol 21, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Paucigranulocytic asthma Immune status WGCNA Hub genes Diseases of the respiratory system RC705-779
spellingShingle	Paucigranulocytic asthma Immune status WGCNA Hub genes Diseases of the respiratory system RC705-779 Min Li Wenye Zhu Chu Wang Yuanyuan Zheng Shibo Sun Yan Fang Zhuang Luo Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
description	Abstract Background Asthma is a heterogeneous disease that can be divided into four inflammatory phenotypes: eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma (MGA), and paucigranulocytic asthma (PGA). While research has mainly focused on EA and NA, the understanding of PGA is limited. In this study, we aimed to identify underlying mechanisms and hub genes of PGA. Methods Based on the dataset from Gene Expression Omnibus(GEO), weighted gene coexpression network analysis (WGCNA), differentially expressed genes (DEGs) analysis and protein–protein interaction (PPI) network analysis were conducted to construct a gene network and to identify key gene modules and hub genes. Functional enrichment analyses were performed to investigate the biological process, pathways and immune status of PGA. The hub genes were validated in a separate dataset. Results Compared to non-PGA, PGA had a different gene expression pattern, in which 449 genes were differentially expressed. One gene module significantly associated with PGA was identified. Intersection between the differentially expressed genes (DEGs) and the genes from the module that were most relevant to PGA were mainly enriched in inflammation and immune response regulation. The single sample Gene Set Enrichment Analysis (ssGSEA) suggested a decreased immune infiltration and function in PGA. Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268. Conclusions Our study characterized distinct gene expression patterns, biological processes and immune status of PGA and identified hub genes, which may improve the understanding of underlying mechanism and provide potential therapeutic targets for PGA.
format	article
author	Min Li Wenye Zhu Chu Wang Yuanyuan Zheng Shibo Sun Yan Fang Zhuang Luo
author_facet	Min Li Wenye Zhu Chu Wang Yuanyuan Zheng Shibo Sun Yan Fang Zhuang Luo
author_sort	Min Li
title	Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
title_short	Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
title_full	Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
title_fullStr	Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
title_full_unstemmed	Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
title_sort	weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma
publisher	BMC
publishDate	2021
url	https://doaj.org/article/eb64ae82e5a643e38060f29d686dd583
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_version_	1718442387854852096

Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma

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