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Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis
BACKGROUND: The study was aimed at finding accurate and effective therapeutic targets and deepening our understanding of the mechanisms of advanced atherosclerosis (AA). METHODS: We downloaded the gene expression datasets GSE28829, GSE120521, and GSE43292 from Gene Expression Omnibus. Weighted gene...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8683248/ https://www.ncbi.nlm.nih.gov/pubmed/34925641 http://dx.doi.org/10.1155/2021/4026604 |
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author | Huo, Tian-ming Wang, Zhi-wei |
author_facet | Huo, Tian-ming Wang, Zhi-wei |
author_sort | Huo, Tian-ming |
collection | PubMed |
description | BACKGROUND: The study was aimed at finding accurate and effective therapeutic targets and deepening our understanding of the mechanisms of advanced atherosclerosis (AA). METHODS: We downloaded the gene expression datasets GSE28829, GSE120521, and GSE43292 from Gene Expression Omnibus. Weighted gene coexpression network analysis (WGCNA) was performed for GSE28829, and functional enrichment analysis and protein–protein interaction network analysis were conducted on the key module. Significant genes in the key module were analyzed by molecular complex detection, and genes in the most important subnetwork were defined as hub genes. Multiple dataset analyses for hub genes were conducted. Genes that overlapped between hub genes and differentially expressed genes (DEGs) of GSE28829 and GSE120521 were defined as key genes. Further validation for key genes was performed using GSE28829 and GSE43292. Gene set enrichment analysis (GSEA) was applied to key genes. RESULTS: A total of 77 significant genes in the key module of GSE28829 were screened out that were mainly associated with inflammation and immunity. The subnetwork was obtained from significant genes, and 18 genes in this module were defined as hub genes, which were related to immunity and expressed in multiple diseases, particularly systemic lupus erythematosus. Some hub genes were regulated by SPI1 and associated with the blood, spleen, and lung. After overlapping with DEGs of GSE28829 and GSE120521, a total of 10 genes (HCK, ITGAM, CTSS, TYROBP, LAPTM5, FCER1G, ITGB2, NCF2, AIF1, and CD86) were identified as key genes. All key genes were validated and evaluated successfully and were related to immune response pathways. CONCLUSION: Our study suggests that the key genes related to immune and inflammatory responses are involved in the development of AA. This may deepen our understanding of the mechanisms of and provide valuable therapeutic targets for AA. |
format | Online Article Text |
id | pubmed-8683248 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Hindawi |
record_format | MEDLINE/PubMed |
spelling | pubmed-86832482021-12-18 Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis Huo, Tian-ming Wang, Zhi-wei Dis Markers Research Article BACKGROUND: The study was aimed at finding accurate and effective therapeutic targets and deepening our understanding of the mechanisms of advanced atherosclerosis (AA). METHODS: We downloaded the gene expression datasets GSE28829, GSE120521, and GSE43292 from Gene Expression Omnibus. Weighted gene coexpression network analysis (WGCNA) was performed for GSE28829, and functional enrichment analysis and protein–protein interaction network analysis were conducted on the key module. Significant genes in the key module were analyzed by molecular complex detection, and genes in the most important subnetwork were defined as hub genes. Multiple dataset analyses for hub genes were conducted. Genes that overlapped between hub genes and differentially expressed genes (DEGs) of GSE28829 and GSE120521 were defined as key genes. Further validation for key genes was performed using GSE28829 and GSE43292. Gene set enrichment analysis (GSEA) was applied to key genes. RESULTS: A total of 77 significant genes in the key module of GSE28829 were screened out that were mainly associated with inflammation and immunity. The subnetwork was obtained from significant genes, and 18 genes in this module were defined as hub genes, which were related to immunity and expressed in multiple diseases, particularly systemic lupus erythematosus. Some hub genes were regulated by SPI1 and associated with the blood, spleen, and lung. After overlapping with DEGs of GSE28829 and GSE120521, a total of 10 genes (HCK, ITGAM, CTSS, TYROBP, LAPTM5, FCER1G, ITGB2, NCF2, AIF1, and CD86) were identified as key genes. All key genes were validated and evaluated successfully and were related to immune response pathways. CONCLUSION: Our study suggests that the key genes related to immune and inflammatory responses are involved in the development of AA. This may deepen our understanding of the mechanisms of and provide valuable therapeutic targets for AA. Hindawi 2021-12-10 /pmc/articles/PMC8683248/ /pubmed/34925641 http://dx.doi.org/10.1155/2021/4026604 Text en Copyright © 2021 Tian-ming Huo and Zhi-wei Wang. https://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 Huo, Tian-ming Wang, Zhi-wei Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis |
title | Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis |
title_full | Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis |
title_fullStr | Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis |
title_full_unstemmed | Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis |
title_short | Comprehensive Analysis to Identify Key Genes Involved in Advanced Atherosclerosis |
title_sort | comprehensive analysis to identify key genes involved in advanced atherosclerosis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8683248/ https://www.ncbi.nlm.nih.gov/pubmed/34925641 http://dx.doi.org/10.1155/2021/4026604 |
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