Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease

Abstract This investigation seeks to dissect coronary artery disease molecular target candidates along with its underlying molecular mechanisms. Data on patients with CAD across three separate array data sets, GSE66360, GSE19339 and GSE97320 were extracted. The gene expression profiles were obtained...

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Autores principales:	Peng-Fei Zheng, Lu-Zhu Chen, Yao-Zong Guan, Peng Liu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cc9ee81cf5f641c2ac5cdba92afe08c2
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spelling	oai:doaj.org-article:cc9ee81cf5f641c2ac5cdba92afe08c22021-12-02T14:02:55ZWeighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease10.1038/s41598-021-86207-02045-2322https://doaj.org/article/cc9ee81cf5f641c2ac5cdba92afe08c22021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86207-0https://doaj.org/toc/2045-2322Abstract This investigation seeks to dissect coronary artery disease molecular target candidates along with its underlying molecular mechanisms. Data on patients with CAD across three separate array data sets, GSE66360, GSE19339 and GSE97320 were extracted. The gene expression profiles were obtained by normalizing and removing the differences between the three data sets, and important modules linked to coronary heart disease were identified using weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and genomes (KEGG) pathway enrichment analyses were applied in order to identify statistically significant genetic modules with the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool (version 6.8; http://david.abcc.ncifcrf.gov ). The online STRING tool was used to construct a protein–protein interaction (PPI) network, followed by the use of Molecular Complex Detection (MCODE) plug-ins in Cytoscape software to identify hub genes. Two significant modules (green-yellow and magenta) were identified in the CAD samples. Genes in the magenta module were noted to be involved in inflammatory and immune-related pathways, based on GO and KEGG enrichment analyses. After the MCODE analysis, two different MCODE complexes were identified in the magenta module, and four hub genes (ITGAM, degree = 39; CAMP, degree = 37; TYROBP, degree = 28; ICAM1, degree = 18) were uncovered to be critical players in mediating CAD. Independent verification data as well as our RT-qPCR results were highly consistent with the above finding. ITGAM, CAMP, TYROBP and ICAM1 are potential targets in CAD. The underlying mechanism may be related to the transendothelial migration of leukocytes and the immune response.Peng-Fei ZhengLu-Zhu ChenYao-Zong GuanPeng LiuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Peng-Fei Zheng Lu-Zhu Chen Yao-Zong Guan Peng Liu Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
description	Abstract This investigation seeks to dissect coronary artery disease molecular target candidates along with its underlying molecular mechanisms. Data on patients with CAD across three separate array data sets, GSE66360, GSE19339 and GSE97320 were extracted. The gene expression profiles were obtained by normalizing and removing the differences between the three data sets, and important modules linked to coronary heart disease were identified using weighted gene co-expression network analysis (WGCNA). Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and genomes (KEGG) pathway enrichment analyses were applied in order to identify statistically significant genetic modules with the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool (version 6.8; http://david.abcc.ncifcrf.gov ). The online STRING tool was used to construct a protein–protein interaction (PPI) network, followed by the use of Molecular Complex Detection (MCODE) plug-ins in Cytoscape software to identify hub genes. Two significant modules (green-yellow and magenta) were identified in the CAD samples. Genes in the magenta module were noted to be involved in inflammatory and immune-related pathways, based on GO and KEGG enrichment analyses. After the MCODE analysis, two different MCODE complexes were identified in the magenta module, and four hub genes (ITGAM, degree = 39; CAMP, degree = 37; TYROBP, degree = 28; ICAM1, degree = 18) were uncovered to be critical players in mediating CAD. Independent verification data as well as our RT-qPCR results were highly consistent with the above finding. ITGAM, CAMP, TYROBP and ICAM1 are potential targets in CAD. The underlying mechanism may be related to the transendothelial migration of leukocytes and the immune response.
format	article
author	Peng-Fei Zheng Lu-Zhu Chen Yao-Zong Guan Peng Liu
author_facet	Peng-Fei Zheng Lu-Zhu Chen Yao-Zong Guan Peng Liu
author_sort	Peng-Fei Zheng
title	Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
title_short	Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
title_full	Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
title_fullStr	Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
title_full_unstemmed	Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
title_sort	weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cc9ee81cf5f641c2ac5cdba92afe08c2
work_keys_str_mv	AT pengfeizheng weightedgenecoexpressionnetworkanalysisidentifiesspecificmodulesandhubgenesrelatedtocoronaryarterydisease AT luzhuchen weightedgenecoexpressionnetworkanalysisidentifiesspecificmodulesandhubgenesrelatedtocoronaryarterydisease AT yaozongguan weightedgenecoexpressionnetworkanalysisidentifiesspecificmodulesandhubgenesrelatedtocoronaryarterydisease AT pengliu weightedgenecoexpressionnetworkanalysisidentifiesspecificmodulesandhubgenesrelatedtocoronaryarterydisease
_version_	1718392109648576512

Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease

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