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Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing

Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA). We investigated d...

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Detalles Bibliográficos
Autores principales: Yang, Wenhui, Li, Yuan, Song, Xia, Xu, Jun, Xie, Jun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Impact Journals LLC 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432281/
https://www.ncbi.nlm.nih.gov/pubmed/28427159
http://dx.doi.org/10.18632/oncotarget.15721
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author Yang, Wenhui
Li, Yuan
Song, Xia
Xu, Jun
Xie, Jun
author_facet Yang, Wenhui
Li, Yuan
Song, Xia
Xu, Jun
Xie, Jun
author_sort Yang, Wenhui
collection PubMed
description Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA). We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues. Moreover, 169 lncRNAs and 597 mRNAs formed the lncRNA-mRNA co-expression network which consist 766 network nodes and 769 connection edges. Bioinformatics analysis identified these dysregulated lncRNAs were associated with cholesterol homeostasis, insoluble fraction and lipid binding activity and were enriched in complement and coagulation cascades and PPAR signaling pathway. These results uncovered the landscape of iCCA-associated lncRNAs and co-expression network, providing insightful information about dysregulated lncRNAs in iCCA.
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spelling pubmed-54322812017-05-17 Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing Yang, Wenhui Li, Yuan Song, Xia Xu, Jun Xie, Jun Oncotarget Research Paper Long noncoding RNAs (lncRNAs), which are pervasively transcribed in the genome, are emerging in molecular biology as crucial regulators of cancer. RNA-seq data were downloaded from GEO of NCBI and further analyzed to identify novel targets in intrahepatic cholangiocarcinoma (iCCA). We investigated differences in lncRNA and mRNA profiles between 7 pairs of iCCA and adjacent normal tissues. 230 lncRNAs were differentially expressed more than four-fold change in iCCA tissues. Among these, 97 were upregulated and 133 downregulated relatively to normal tissues. Moreover, 169 lncRNAs and 597 mRNAs formed the lncRNA-mRNA co-expression network which consist 766 network nodes and 769 connection edges. Bioinformatics analysis identified these dysregulated lncRNAs were associated with cholesterol homeostasis, insoluble fraction and lipid binding activity and were enriched in complement and coagulation cascades and PPAR signaling pathway. These results uncovered the landscape of iCCA-associated lncRNAs and co-expression network, providing insightful information about dysregulated lncRNAs in iCCA. Impact Journals LLC 2017-02-24 /pmc/articles/PMC5432281/ /pubmed/28427159 http://dx.doi.org/10.18632/oncotarget.15721 Text en Copyright: © 2017 Yang et al. http://creativecommons.org/licenses/by/3.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) (CC-BY), which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Research Paper
Yang, Wenhui
Li, Yuan
Song, Xia
Xu, Jun
Xie, Jun
Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing
title Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing
title_full Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing
title_fullStr Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing
title_full_unstemmed Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing
title_short Genome-wide analysis of long noncoding RNA and mRNA co-expression profile in intrahepatic cholangiocarcinoma tissue by RNA sequencing
title_sort genome-wide analysis of long noncoding rna and mrna co-expression profile in intrahepatic cholangiocarcinoma tissue by rna sequencing
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432281/
https://www.ncbi.nlm.nih.gov/pubmed/28427159
http://dx.doi.org/10.18632/oncotarget.15721
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