Cargando…
Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease
BACKGROUND: Coronary artery disease (CAD) is a type of heart disease with a high morbidity rate. This study is aimed at identifying potential biomarkers closely related to the progression of CAD. MATERIALS AND METHODS: A microarray dataset of GSE59867 was downloaded from a public database, Gene Expr...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7361886/ https://www.ncbi.nlm.nih.gov/pubmed/32695216 http://dx.doi.org/10.1155/2020/8183420 |
_version_ | 1783559412195000320 |
---|---|
author | Wang, Lang Hu, Jun Zhou, Jiali Guo, Fan Yao, Tan Zhang, Liang |
author_facet | Wang, Lang Hu, Jun Zhou, Jiali Guo, Fan Yao, Tan Zhang, Liang |
author_sort | Wang, Lang |
collection | PubMed |
description | BACKGROUND: Coronary artery disease (CAD) is a type of heart disease with a high morbidity rate. This study is aimed at identifying potential biomarkers closely related to the progression of CAD. MATERIALS AND METHODS: A microarray dataset of GSE59867 was downloaded from a public database, Gene Expression Omnibus, which included 46 cases of stable CAD without a history of myocardial infarction (MI), 30 cases of MI without heart failure (HF), and 34 cases of MI with HF. Differentially expressed long noncoding RNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified by the limma package, and functions of DEmRNAs were annotated by Gene Ontology and KEGG pathways. In addition, weighed gene coexpression network analysis (WGCNA) was used to construct a coexpression network of DEmRNAs, and a disease-related lncRNAs-mRNAs-pathway network was constructed. Finally, the datasets of GSE61145 and GSE57338 were used to verify the expression levels of the above highly correlated candidates. RESULTS: A total of 2362 upregulated mRNAs and 2816 downregulated mRNAs, as well as 235 upregulated lncRNAs and 113 downregulated lncRNAs were screened. These genes were significantly enriched in “cytokine-cytokine receptor interaction,” “RIG-I-like receptor signaling pathway,” and “natural killer cell-mediated cytotoxicity.” Five modules including 1201 DEmRNAs were enriched in WGCNA. A coexpression network including 19 DElncRNAs and 413 DEmRNAs was constructed. These genes were significantly enriched in “phosphatidylinositol signaling system,” “insulin signaling pathway,” and “MAPK signaling pathway”. Disease-related gene-pathway network suggested FASN in “insulin signaling pathway,” DGKZ in “phosphatidylinositol signaling system,” and TNFRSF1A in “MAPK signaling pathway” were involved in MI. CONCLUSION: FASN, DGKZ, and TNFRSF1A were revealed to be CAD progression-associated genes by WGCNA coexpression network analysis. |
format | Online Article Text |
id | pubmed-7361886 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Hindawi |
record_format | MEDLINE/PubMed |
spelling | pubmed-73618862020-07-20 Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease Wang, Lang Hu, Jun Zhou, Jiali Guo, Fan Yao, Tan Zhang, Liang Comput Math Methods Med Research Article BACKGROUND: Coronary artery disease (CAD) is a type of heart disease with a high morbidity rate. This study is aimed at identifying potential biomarkers closely related to the progression of CAD. MATERIALS AND METHODS: A microarray dataset of GSE59867 was downloaded from a public database, Gene Expression Omnibus, which included 46 cases of stable CAD without a history of myocardial infarction (MI), 30 cases of MI without heart failure (HF), and 34 cases of MI with HF. Differentially expressed long noncoding RNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified by the limma package, and functions of DEmRNAs were annotated by Gene Ontology and KEGG pathways. In addition, weighed gene coexpression network analysis (WGCNA) was used to construct a coexpression network of DEmRNAs, and a disease-related lncRNAs-mRNAs-pathway network was constructed. Finally, the datasets of GSE61145 and GSE57338 were used to verify the expression levels of the above highly correlated candidates. RESULTS: A total of 2362 upregulated mRNAs and 2816 downregulated mRNAs, as well as 235 upregulated lncRNAs and 113 downregulated lncRNAs were screened. These genes were significantly enriched in “cytokine-cytokine receptor interaction,” “RIG-I-like receptor signaling pathway,” and “natural killer cell-mediated cytotoxicity.” Five modules including 1201 DEmRNAs were enriched in WGCNA. A coexpression network including 19 DElncRNAs and 413 DEmRNAs was constructed. These genes were significantly enriched in “phosphatidylinositol signaling system,” “insulin signaling pathway,” and “MAPK signaling pathway”. Disease-related gene-pathway network suggested FASN in “insulin signaling pathway,” DGKZ in “phosphatidylinositol signaling system,” and TNFRSF1A in “MAPK signaling pathway” were involved in MI. CONCLUSION: FASN, DGKZ, and TNFRSF1A were revealed to be CAD progression-associated genes by WGCNA coexpression network analysis. Hindawi 2020-07-06 /pmc/articles/PMC7361886/ /pubmed/32695216 http://dx.doi.org/10.1155/2020/8183420 Text en Copyright © 2020 Lang Wang et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Wang, Lang Hu, Jun Zhou, Jiali Guo, Fan Yao, Tan Zhang, Liang Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease |
title | Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease |
title_full | Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease |
title_fullStr | Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease |
title_full_unstemmed | Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease |
title_short | Weighed Gene Coexpression Network Analysis Screens the Potential Long Noncoding RNAs and Genes Associated with Progression of Coronary Artery Disease |
title_sort | weighed gene coexpression network analysis screens the potential long noncoding rnas and genes associated with progression of coronary artery disease |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7361886/ https://www.ncbi.nlm.nih.gov/pubmed/32695216 http://dx.doi.org/10.1155/2020/8183420 |
work_keys_str_mv | AT wanglang weighedgenecoexpressionnetworkanalysisscreensthepotentiallongnoncodingrnasandgenesassociatedwithprogressionofcoronaryarterydisease AT hujun weighedgenecoexpressionnetworkanalysisscreensthepotentiallongnoncodingrnasandgenesassociatedwithprogressionofcoronaryarterydisease AT zhoujiali weighedgenecoexpressionnetworkanalysisscreensthepotentiallongnoncodingrnasandgenesassociatedwithprogressionofcoronaryarterydisease AT guofan weighedgenecoexpressionnetworkanalysisscreensthepotentiallongnoncodingrnasandgenesassociatedwithprogressionofcoronaryarterydisease AT yaotan weighedgenecoexpressionnetworkanalysisscreensthepotentiallongnoncodingrnasandgenesassociatedwithprogressionofcoronaryarterydisease AT zhangliang weighedgenecoexpressionnetworkanalysisscreensthepotentiallongnoncodingrnasandgenesassociatedwithprogressionofcoronaryarterydisease |