Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG
Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal...
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| Veröffentlicht in: | Genetica 2022-02, Vol.150 (1), p.41-50 |
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| creator | Ding, Yiming Liu, Hanjie Zhang, Chuanbao Bao, Zhaoshi Yu, Shuqing |
| description | Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan–Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG. |
| doi_str_mv | 10.1007/s10709-021-00145-3 |
| format | Article |
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However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan–Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG.</description><identifier>ISSN: 0016-6707</identifier><identifier>EISSN: 1573-6857</identifier><identifier>DOI: 10.1007/s10709-021-00145-3</identifier><identifier>PMID: 34993720</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Animal Genetics and Genomics ; Biological activity ; Biomedical and Life Sciences ; Cancer ; Computer applications ; Encyclopedias ; Evolutionary Biology ; Gene Regulatory Networks ; Gene sequencing ; Genes ; Genomes ; Glioma ; Human Genetics ; Humans ; Life Sciences ; Microbial Genetics and Genomics ; MicroRNAs ; MicroRNAs - genetics ; MicroRNAs - metabolism ; miRNA ; mRNA ; Non-coding RNA ; Original Paper ; Pathogenesis ; Plant Genetics and Genomics ; Ribonucleic acid ; RNA ; RNA, Long Noncoding - genetics ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; Survival ; Survival analysis ; Tumors</subject><ispartof>Genetica, 2022-02, Vol.150 (1), p.41-50</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Switzerland AG 2021</rights><rights>2021. 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However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan–Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG.</description><subject>Animal Genetics and Genomics</subject><subject>Biological activity</subject><subject>Biomedical and Life Sciences</subject><subject>Cancer</subject><subject>Computer applications</subject><subject>Encyclopedias</subject><subject>Evolutionary Biology</subject><subject>Gene Regulatory Networks</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Glioma</subject><subject>Human Genetics</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Microbial Genetics and Genomics</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>miRNA</subject><subject>mRNA</subject><subject>Non-coding RNA</subject><subject>Original Paper</subject><subject>Pathogenesis</subject><subject>Plant Genetics and Genomics</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Long Noncoding - 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Academic</collection><jtitle>Genetica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ding, Yiming</au><au>Liu, Hanjie</au><au>Zhang, Chuanbao</au><au>Bao, Zhaoshi</au><au>Yu, Shuqing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG</atitle><jtitle>Genetica</jtitle><stitle>Genetica</stitle><addtitle>Genetica</addtitle><date>2022-02-01</date><risdate>2022</risdate><volume>150</volume><issue>1</issue><spage>41</spage><epage>50</epage><pages>41-50</pages><issn>0016-6707</issn><eissn>1573-6857</eissn><abstract>Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan–Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>34993720</pmid><doi>10.1007/s10709-021-00145-3</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0001-8012-2398</orcidid></addata></record> |
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| subjects | Animal Genetics and Genomics Biological activity Biomedical and Life Sciences Cancer Computer applications Encyclopedias Evolutionary Biology Gene Regulatory Networks Gene sequencing Genes Genomes Glioma Human Genetics Humans Life Sciences Microbial Genetics and Genomics MicroRNAs MicroRNAs - genetics MicroRNAs - metabolism miRNA mRNA Non-coding RNA Original Paper Pathogenesis Plant Genetics and Genomics Ribonucleic acid RNA RNA, Long Noncoding - genetics RNA, Messenger - genetics RNA, Messenger - metabolism Survival Survival analysis Tumors |
| title | Comprehensive analysis of the LncRNAs, MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG |
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