A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients

Abstract Cholangiocarcinoma (CCA) is a group of malignancies emerging in the biliary tree and is associated with a poor patient prognosis. Although the anatomical location is the only worldwide accepted classification basis, it still has bias. The current study integrates the whole-genome expression...

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Autores principales:	Hongguang Li, Lingxin Qu, Haibin Zhang, Jun Liu, Xiaolu Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cd2456d0dca74787b846947e6db0d79c
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spelling	oai:doaj.org-article:cd2456d0dca74787b846947e6db0d79c2021-12-02T16:10:38ZA comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients10.1038/s41598-021-93250-42045-2322https://doaj.org/article/cd2456d0dca74787b846947e6db0d79c2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93250-4https://doaj.org/toc/2045-2322Abstract Cholangiocarcinoma (CCA) is a group of malignancies emerging in the biliary tree and is associated with a poor patient prognosis. Although the anatomical location is the only worldwide accepted classification basis, it still has bias. The current study integrates the whole-genome expression data from several big cohorts in the literature, to screen and provide a comprehensive bioinformatic analysis, in order to better classify molecular subtypes and explore an underlying cluster mechanism related to anatomy and geographical regions. Differentially expressed protein-coding genes (DEGs) were identified for CCA as well as subtypes. Biological function enrichment analysis—Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis—was applied and identified different DEGs enriched signaling pathways in CCA subtypes. A co-expression network was presented by Weighted gene co-expression network analysis package and modules related to specific phenotypes were identified. Combined with DEGs, hub genes in the given module were demonstrated through protein–protein interaction network analysis. Finally, DEGs which significantly related to patient overall survival and disease-free survival time were selected, including ARHGAP21, SCP2, UBIAD1, TJP2, RAP1A and HDAC9.Hongguang LiLingxin QuHaibin ZhangJun LiuXiaolu ZhangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hongguang Li Lingxin Qu Haibin Zhang Jun Liu Xiaolu Zhang A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
description	Abstract Cholangiocarcinoma (CCA) is a group of malignancies emerging in the biliary tree and is associated with a poor patient prognosis. Although the anatomical location is the only worldwide accepted classification basis, it still has bias. The current study integrates the whole-genome expression data from several big cohorts in the literature, to screen and provide a comprehensive bioinformatic analysis, in order to better classify molecular subtypes and explore an underlying cluster mechanism related to anatomy and geographical regions. Differentially expressed protein-coding genes (DEGs) were identified for CCA as well as subtypes. Biological function enrichment analysis—Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis—was applied and identified different DEGs enriched signaling pathways in CCA subtypes. A co-expression network was presented by Weighted gene co-expression network analysis package and modules related to specific phenotypes were identified. Combined with DEGs, hub genes in the given module were demonstrated through protein–protein interaction network analysis. Finally, DEGs which significantly related to patient overall survival and disease-free survival time were selected, including ARHGAP21, SCP2, UBIAD1, TJP2, RAP1A and HDAC9.
format	article
author	Hongguang Li Lingxin Qu Haibin Zhang Jun Liu Xiaolu Zhang
author_facet	Hongguang Li Lingxin Qu Haibin Zhang Jun Liu Xiaolu Zhang
author_sort	Hongguang Li
title	A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
title_short	A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
title_full	A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
title_fullStr	A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
title_full_unstemmed	A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
title_sort	comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cd2456d0dca74787b846947e6db0d79c
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A comprehensive transcriptomic landscape of cholangiocarcinoma based on bioinformatics analysis from large cohort of patients

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