Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction

Abstract Functioning as miRNA sponges, long non-coding RNA (lncRNA) exert its pharmacological action via regulating expression of protein-coding genes. However, the lncRNA-mediated ceRNA in cerebral Infarction (CI) remains unclear. In this study, the expression recordsets of mRNA, lncRNA and miRNA o...

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Autores principales:	Jun-Bo Zou, Hong-Bo Chai, Xiao-Fei Zhang, Dong-Yan Guo, Jia Tai, Yu Wang, Yu-Lin Liang, Fang Wang, Jiang-Xue Cheng, Jing Wang, Ya-Jun Shi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a37d41c1d0cf4ea4b81a16e72217cc69
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spelling	oai:doaj.org-article:a37d41c1d0cf4ea4b81a16e72217cc692021-12-02T15:09:15ZReconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction10.1038/s41598-019-48435-32045-2322https://doaj.org/article/a37d41c1d0cf4ea4b81a16e72217cc692019-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-48435-3https://doaj.org/toc/2045-2322Abstract Functioning as miRNA sponges, long non-coding RNA (lncRNA) exert its pharmacological action via regulating expression of protein-coding genes. However, the lncRNA-mediated ceRNA in cerebral Infarction (CI) remains unclear. In this study, the expression recordsets of mRNA, lncRNA and miRNA of CI samples were obtained from the NCBI GEO datasets separately. The differentially expressed lncRNAs (DELs), miRNAs (DEMis) and mRNAs (DEMs) were identified by limma package in R platform. A total of 267 DELs, 26 DEMis, and 760 DEMs were identified as differentially expressed profiles, with which we constructed the ceRNA network composed of DELs-DEMis-DEMs. Further, clusterProfiler package in R platform is employed for performing Gene Ontology (GO) and KEGG pathway analysis. An aberrant ceRNA network was constructed according to node degrees in CI, including 28 DELs, 19 DEMs and 12 DEMis, from which we extracted the core network, in which 9 nodes were recognized as kernel genes including Tspan3, Eif4a2, rno-miR-208a-3p, rno-miR-194-5p, Pdpn, H3f3b, Stat3, Cd63 and Sdc4. Finally, with the DELs-DEMis-DEMs ceRNA network provided above, we can improve our understanding of the pathogenesis of CI mediated by lncRNA.Jun-Bo ZouHong-Bo ChaiXiao-Fei ZhangDong-Yan GuoJia TaiYu WangYu-Lin LiangFang WangJiang-Xue ChengJing WangYa-Jun ShiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-13 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jun-Bo Zou Hong-Bo Chai Xiao-Fei Zhang Dong-Yan Guo Jia Tai Yu Wang Yu-Lin Liang Fang Wang Jiang-Xue Cheng Jing Wang Ya-Jun Shi Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
description	Abstract Functioning as miRNA sponges, long non-coding RNA (lncRNA) exert its pharmacological action via regulating expression of protein-coding genes. However, the lncRNA-mediated ceRNA in cerebral Infarction (CI) remains unclear. In this study, the expression recordsets of mRNA, lncRNA and miRNA of CI samples were obtained from the NCBI GEO datasets separately. The differentially expressed lncRNAs (DELs), miRNAs (DEMis) and mRNAs (DEMs) were identified by limma package in R platform. A total of 267 DELs, 26 DEMis, and 760 DEMs were identified as differentially expressed profiles, with which we constructed the ceRNA network composed of DELs-DEMis-DEMs. Further, clusterProfiler package in R platform is employed for performing Gene Ontology (GO) and KEGG pathway analysis. An aberrant ceRNA network was constructed according to node degrees in CI, including 28 DELs, 19 DEMs and 12 DEMis, from which we extracted the core network, in which 9 nodes were recognized as kernel genes including Tspan3, Eif4a2, rno-miR-208a-3p, rno-miR-194-5p, Pdpn, H3f3b, Stat3, Cd63 and Sdc4. Finally, with the DELs-DEMis-DEMs ceRNA network provided above, we can improve our understanding of the pathogenesis of CI mediated by lncRNA.
format	article
author	Jun-Bo Zou Hong-Bo Chai Xiao-Fei Zhang Dong-Yan Guo Jia Tai Yu Wang Yu-Lin Liang Fang Wang Jiang-Xue Cheng Jing Wang Ya-Jun Shi
author_facet	Jun-Bo Zou Hong-Bo Chai Xiao-Fei Zhang Dong-Yan Guo Jia Tai Yu Wang Yu-Lin Liang Fang Wang Jiang-Xue Cheng Jing Wang Ya-Jun Shi
author_sort	Jun-Bo Zou
title	Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
title_short	Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
title_full	Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
title_fullStr	Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
title_full_unstemmed	Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction
title_sort	reconstruction of the lncrna-mirna-mrna network based on competitive endogenous rna reveal functional lncrnas in cerebral infarction
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/a37d41c1d0cf4ea4b81a16e72217cc69
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Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral Infarction

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