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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| Format: | Article |
| Language: | English |
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Nature Portfolio
2019-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-019-48435-3 |
| _version_ | 1818345868939493376 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T17:09:13Z |
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| id | doaj.art-a37d41c1d0cf4ea4b81a16e72217cc69 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-13T17:09:13Z |
| publishDate | 2019-08-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj.art-a37d41c1d0cf4ea4b81a16e72217cc692022-12-21T23:37:37ZengNature PortfolioScientific Reports2045-23222019-08-019111310.1038/s41598-019-48435-3Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in Cerebral InfarctionJun-Bo Zou0Hong-Bo Chai1Xiao-Fei Zhang2Dong-Yan Guo3Jia Tai4Yu Wang5Yu-Lin Liang6Fang Wang7Jiang-Xue Cheng8Jing Wang9Ya-Jun Shi10Shaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineThe first affiliated Hospital of Hunan University of MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineKey laboratory of Modern Prepararation of Traditional Chinese Medicine, Ministry of Education, Jiangxi University of Traditional Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineShaanxi Province Key Laboratory of New Drugs and Chinese Medicine Foundation Research,Pharmacy College, Shaanxi University of Chinese MedicineAbstract 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.https://doi.org/10.1038/s41598-019-48435-3 |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-019-48435-3 |
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