Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database
Abstract Background Ischemic cardiomyopathy (ICM) is one of the most usual causes of death worldwide. This study aimed to find the candidate gene for ICM. Methods We studied differentially expressed genes (DEGs) in ICM compared to healthy control. According to these DEGs, we carried out the function...
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doaj-26460fbe7cc9490c8eb3c999b8722d922020-11-25T03:50:46ZengBMCBMC Cardiovascular Disorders1471-22612020-07-0120111010.1186/s12872-020-01596-wIdentification of candidate genes in ischemic cardiomyopathy by gene expression omnibus databaseHaiming Dang0Yicong Ye1Xiliang Zhao2Yong Zeng3Department of cardiac surgery, Capital medical university, Beijing Anzhen hospitalDepartment of cardiology, Capital medical university, Beijing Anzhen hospitalDepartment of cardiology, Capital medical university, Beijing Anzhen hospitalDepartment of cardiology, Capital medical university, Beijing Anzhen hospitalAbstract Background Ischemic cardiomyopathy (ICM) is one of the most usual causes of death worldwide. This study aimed to find the candidate gene for ICM. Methods We studied differentially expressed genes (DEGs) in ICM compared to healthy control. According to these DEGs, we carried out the functional annotation, protein-protein interaction (PPI) network and transcriptional regulatory network constructions. The expression of selected candidate genes were confirmed using a published dataset and Quantitative real time polymerase chain reaction (qRT-PCR). Results From three Gene Expression Omnibus (GEO) datasets, we acquired 1081 DEGs (578 up-regulated and 503 down-regulated genes) between ICM and healthy control. The functional annotation analysis revealed that cardiac muscle contraction, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy were significantly enriched pathways in ICM. SNRPB, BLM, RRS1, CDK2, BCL6, BCL2L1, FKBP5, IPO7, TUBB4B and ATP1A1 were considered the hub proteins. PALLD, THBS4, ATP1A1, NFASC, FKBP5, ECM2 and BCL2L1 were top six transcription factors (TFs) with the most downstream genes. The expression of 6 DEGs (MYH6, THBS4, BCL6, BLM, IPO7 and SERPINA3) were consistent with our integration analysis and GSE116250 validation results. Conclusions The candidate DEGs and TFs may be related to the ICM process. This study provided novel perspective for understanding mechanism and exploiting new therapeutic means for ICM.http://link.springer.com/article/10.1186/s12872-020-01596-wIschemic cardiomyopathyDifferentially expressed genesGene expression omnibus datasetsIntegrated analysis |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Haiming Dang Yicong Ye Xiliang Zhao Yong Zeng |
spellingShingle |
Haiming Dang Yicong Ye Xiliang Zhao Yong Zeng Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database BMC Cardiovascular Disorders Ischemic cardiomyopathy Differentially expressed genes Gene expression omnibus datasets Integrated analysis |
author_facet |
Haiming Dang Yicong Ye Xiliang Zhao Yong Zeng |
author_sort |
Haiming Dang |
title |
Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database |
title_short |
Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database |
title_full |
Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database |
title_fullStr |
Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database |
title_full_unstemmed |
Identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database |
title_sort |
identification of candidate genes in ischemic cardiomyopathy by gene expression omnibus database |
publisher |
BMC |
series |
BMC Cardiovascular Disorders |
issn |
1471-2261 |
publishDate |
2020-07-01 |
description |
Abstract Background Ischemic cardiomyopathy (ICM) is one of the most usual causes of death worldwide. This study aimed to find the candidate gene for ICM. Methods We studied differentially expressed genes (DEGs) in ICM compared to healthy control. According to these DEGs, we carried out the functional annotation, protein-protein interaction (PPI) network and transcriptional regulatory network constructions. The expression of selected candidate genes were confirmed using a published dataset and Quantitative real time polymerase chain reaction (qRT-PCR). Results From three Gene Expression Omnibus (GEO) datasets, we acquired 1081 DEGs (578 up-regulated and 503 down-regulated genes) between ICM and healthy control. The functional annotation analysis revealed that cardiac muscle contraction, hypertrophic cardiomyopathy, arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy were significantly enriched pathways in ICM. SNRPB, BLM, RRS1, CDK2, BCL6, BCL2L1, FKBP5, IPO7, TUBB4B and ATP1A1 were considered the hub proteins. PALLD, THBS4, ATP1A1, NFASC, FKBP5, ECM2 and BCL2L1 were top six transcription factors (TFs) with the most downstream genes. The expression of 6 DEGs (MYH6, THBS4, BCL6, BLM, IPO7 and SERPINA3) were consistent with our integration analysis and GSE116250 validation results. Conclusions The candidate DEGs and TFs may be related to the ICM process. This study provided novel perspective for understanding mechanism and exploiting new therapeutic means for ICM. |
topic |
Ischemic cardiomyopathy Differentially expressed genes Gene expression omnibus datasets Integrated analysis |
url |
http://link.springer.com/article/10.1186/s12872-020-01596-w |
work_keys_str_mv |
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