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Assessing the impact of mutations found in next generation sequencing data over human signaling pathways

Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic nature of many diseases or traits. Here we present PATH...

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Autores principales: Hernansaiz-Ballesteros, Rosa D., Salavert, Francisco, Sebastián-León, Patricia, Alemán, Alejandro, Medina, Ignacio, Dopazo, Joaquín
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489259/
https://www.ncbi.nlm.nih.gov/pubmed/25883139
http://dx.doi.org/10.1093/nar/gkv349
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author Hernansaiz-Ballesteros, Rosa D.
Salavert, Francisco
Sebastián-León, Patricia
Alemán, Alejandro
Medina, Ignacio
Dopazo, Joaquín
author_facet Hernansaiz-Ballesteros, Rosa D.
Salavert, Francisco
Sebastián-León, Patricia
Alemán, Alejandro
Medina, Ignacio
Dopazo, Joaquín
author_sort Hernansaiz-Ballesteros, Rosa D.
collection PubMed
description Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic nature of many diseases or traits. Here we present PATHiVar, a web-based tool that integrates genomic variation data with gene expression tissue information. PATHiVar constitutes a new generation of genomic data analysis methods that allow studying variants found in next generation sequencing experiment in the context of signaling pathways. Simple Boolean models of pathways provide detailed descriptions of the impact of mutations in cell functionality so as, recurrences in functionality failures can easily be related to diseases, even if they are produced by mutations in different genes. Patterns of changes in signal transmission circuits, often unpredictable from individual genes mutated, correspond to patterns of affected functionalities that can be related to complex traits such as disease progression, drug response, etc. PATHiVar is available at: http://pathivar.babelomics.org.
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spelling pubmed-44892592015-07-07 Assessing the impact of mutations found in next generation sequencing data over human signaling pathways Hernansaiz-Ballesteros, Rosa D. Salavert, Francisco Sebastián-León, Patricia Alemán, Alejandro Medina, Ignacio Dopazo, Joaquín Nucleic Acids Res Web Server issue Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic nature of many diseases or traits. Here we present PATHiVar, a web-based tool that integrates genomic variation data with gene expression tissue information. PATHiVar constitutes a new generation of genomic data analysis methods that allow studying variants found in next generation sequencing experiment in the context of signaling pathways. Simple Boolean models of pathways provide detailed descriptions of the impact of mutations in cell functionality so as, recurrences in functionality failures can easily be related to diseases, even if they are produced by mutations in different genes. Patterns of changes in signal transmission circuits, often unpredictable from individual genes mutated, correspond to patterns of affected functionalities that can be related to complex traits such as disease progression, drug response, etc. PATHiVar is available at: http://pathivar.babelomics.org. Oxford University Press 2015-07-01 2015-04-16 /pmc/articles/PMC4489259/ /pubmed/25883139 http://dx.doi.org/10.1093/nar/gkv349 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server issue
Hernansaiz-Ballesteros, Rosa D.
Salavert, Francisco
Sebastián-León, Patricia
Alemán, Alejandro
Medina, Ignacio
Dopazo, Joaquín
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
title Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
title_full Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
title_fullStr Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
title_full_unstemmed Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
title_short Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
title_sort assessing the impact of mutations found in next generation sequencing data over human signaling pathways
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489259/
https://www.ncbi.nlm.nih.gov/pubmed/25883139
http://dx.doi.org/10.1093/nar/gkv349
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