Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis

BACKGROUND: Asthma is a chronic lung disease characterized by reversible inflammation of the airways. The imbalance of Th1/Th2 cells plays a significant role in the mechanisms of asthma. The aim of this study was to identify asthma-related key genes and functionally enriched pathways in a Th2-high g...

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Autores principales: Cao, Yao, Wu, Yi, Lin, Li, Yang, Lin, Peng, Xin, Chen, Lina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Research
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9097074/
https://www.ncbi.nlm.nih.gov/pubmed/35550122
http://dx.doi.org/10.1186/s12920-022-01241-9
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author Cao, Yao
Wu, Yi
Lin, Li
Yang, Lin
Peng, Xin
Chen, Lina
author_facet Cao, Yao
Wu, Yi
Lin, Li
Yang, Lin
Peng, Xin
Chen, Lina
author_sort Cao, Yao
collection PubMed
description BACKGROUND: Asthma is a chronic lung disease characterized by reversible inflammation of the airways. The imbalance of Th1/Th2 cells plays a significant role in the mechanisms of asthma. The aim of this study was to identify asthma-related key genes and functionally enriched pathways in a Th2-high group by using weighted gene coexpression network analysis (WGCNA). METHODS: The gene expression profiles of GSE4302, which included 42 asthma patients and 28 controls, were selected from the Gene Expression Omnibus (GEO). A gene network was constructed, and genes were classified into different modules using WGCNA. Gene ontology (GO) was performed to further explore the potential function of the genes in the most related module. In addition, the expression profile and diagnostic capacity (ROC curve) of hub genes of interest were verified by dataset GSE67472. RESULTS: In dataset GSE4302, subjects with asthma were divided into Th2-high and Th2-low groups according to the expression of the SERPINB2, POSTN and CLCA1 genes. A weighted gene coexpression network was constructed, and genes were classified into 7 modules. Among them, the red module was most closely associated with Th2-high asthma, which contained 60 genes. These genes were significantly enriched in different biological processes and molecular functions. A total of 8 hub genes (TPSB2, CPA3, ITLN1, CST1, SERPINB10, CEACAM5, CHD26 and P2RY14) were identified, and the expression levels of these genes (except TPSB2) were confirmed in dataset GSE67472. ROC curve analysis validated that the expression of these 8 genes exhibited excellent diagnostic efficiency for Th2-high asthma and Th2-low asthma. CONCLUSIONS: The study provides a novel perspective on Th2-high asthma by WGCNA, and the hub genes and potential pathways involved may be beneficial for the diagnosis and management of Th2-high asthma. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-022-01241-9.
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spelling pubmed-90970742022-05-13 Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis Cao, Yao Wu, Yi Lin, Li Yang, Lin Peng, Xin Chen, Lina BMC Med Genomics Research BACKGROUND: Asthma is a chronic lung disease characterized by reversible inflammation of the airways. The imbalance of Th1/Th2 cells plays a significant role in the mechanisms of asthma. The aim of this study was to identify asthma-related key genes and functionally enriched pathways in a Th2-high group by using weighted gene coexpression network analysis (WGCNA). METHODS: The gene expression profiles of GSE4302, which included 42 asthma patients and 28 controls, were selected from the Gene Expression Omnibus (GEO). A gene network was constructed, and genes were classified into different modules using WGCNA. Gene ontology (GO) was performed to further explore the potential function of the genes in the most related module. In addition, the expression profile and diagnostic capacity (ROC curve) of hub genes of interest were verified by dataset GSE67472. RESULTS: In dataset GSE4302, subjects with asthma were divided into Th2-high and Th2-low groups according to the expression of the SERPINB2, POSTN and CLCA1 genes. A weighted gene coexpression network was constructed, and genes were classified into 7 modules. Among them, the red module was most closely associated with Th2-high asthma, which contained 60 genes. These genes were significantly enriched in different biological processes and molecular functions. A total of 8 hub genes (TPSB2, CPA3, ITLN1, CST1, SERPINB10, CEACAM5, CHD26 and P2RY14) were identified, and the expression levels of these genes (except TPSB2) were confirmed in dataset GSE67472. ROC curve analysis validated that the expression of these 8 genes exhibited excellent diagnostic efficiency for Th2-high asthma and Th2-low asthma. CONCLUSIONS: The study provides a novel perspective on Th2-high asthma by WGCNA, and the hub genes and potential pathways involved may be beneficial for the diagnosis and management of Th2-high asthma. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-022-01241-9. BioMed Central 2022-05-12 /pmc/articles/PMC9097074/ /pubmed/35550122 http://dx.doi.org/10.1186/s12920-022-01241-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visithttp://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Cao, Yao
Wu, Yi
Lin, Li
Yang, Lin
Peng, Xin
Chen, Lina
Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis
title Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis
title_full Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis
title_fullStr Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis
title_full_unstemmed Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis
title_short Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis
title_sort identifying key genes and functionally enriched pathways in th2-high asthma by weighted gene co-expression network analysis
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9097074/
https://www.ncbi.nlm.nih.gov/pubmed/35550122
http://dx.doi.org/10.1186/s12920-022-01241-9
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