A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>

ABSTRACT Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The steady accumulation of these data sets now provides a unique opportunity for in silico hypothesis generation via coex...

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Autores principales:	Cory D. DuPai, Claus O. Wilke, Bryan W. Davies
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Vibrio cholerae computational biology Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/08b1847653c9482d84f897afde81eab1
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spelling	oai:doaj.org-article:08b1847653c9482d84f897afde81eab12021-12-02T19:47:35ZA Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>10.1128/mSystems.00550-202379-5077https://doaj.org/article/08b1847653c9482d84f897afde81eab12020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00550-20https://doaj.org/toc/2379-5077ABSTRACT Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The steady accumulation of these data sets now provides a unique opportunity for in silico hypothesis generation via coexpression analysis. Here, we leverage all published V. cholerae RNA sequencing data, in combination with select data from other platforms, to generate a gene coexpression network that validates known gene interactions and identifies novel genetic partners across the entire V. cholerae genome. This network provides direct insights into genes influencing pathogenicity, metabolism, and transcriptional regulation, further clarifies results from previous sequencing experiments in V. cholerae (e.g., transposon insertion sequencing [Tn-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]), and expands upon microarray-based findings in related Gram-negative bacteria. IMPORTANCE Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution.Cory D. DuPaiClaus O. WilkeBryan W. DaviesAmerican Society for MicrobiologyarticleVibrio choleraecomputational biologyMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Vibrio cholerae computational biology Microbiology QR1-502
spellingShingle	Vibrio cholerae computational biology Microbiology QR1-502 Cory D. DuPai Claus O. Wilke Bryan W. Davies A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>
description	ABSTRACT Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high-throughput sequencing data to drive molecular analyses. The steady accumulation of these data sets now provides a unique opportunity for in silico hypothesis generation via coexpression analysis. Here, we leverage all published V. cholerae RNA sequencing data, in combination with select data from other platforms, to generate a gene coexpression network that validates known gene interactions and identifies novel genetic partners across the entire V. cholerae genome. This network provides direct insights into genes influencing pathogenicity, metabolism, and transcriptional regulation, further clarifies results from previous sequencing experiments in V. cholerae (e.g., transposon insertion sequencing [Tn-seq] and chromatin immunoprecipitation sequencing [ChIP-seq]), and expands upon microarray-based findings in related Gram-negative bacteria. IMPORTANCE Cholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite the importance of this pathogen, roughly one-third of V. cholerae genes are functionally unannotated, leaving large gaps in our understanding of this microbe. Through coexpression network analysis of existing RNA sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution.
format	article
author	Cory D. DuPai Claus O. Wilke Bryan W. Davies
author_facet	Cory D. DuPai Claus O. Wilke Bryan W. Davies
author_sort	Cory D. DuPai
title	A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>
title_short	A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>
title_full	A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>
title_fullStr	A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>
title_full_unstemmed	A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>
title_sort	comprehensive coexpression network analysis in <named-content content-type="genus-species">vibrio cholerae</named-content>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/08b1847653c9482d84f897afde81eab1
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A Comprehensive Coexpression Network Analysis in <named-content content-type="genus-species">Vibrio cholerae</named-content>

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