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

TitleAssessing the impact of mutations found in next generation sequencing data over human signaling pathways.
Publication TypeJournal Article
Year of Publication2015
AuthorsHernansaiz-Ballesteros, RD, Salavert, F, Sebastián-Leon, P, Alemán, A, Medina, I, Dopazo, J
JournalNucleic Acids Res
Volume43
IssueW1
PaginationW270-5
Date Published2015 Jul 01
ISSN1362-4962
Keywordsgene expression; Genomics; High-Throughput Nucleotide Sequencing; Humans; Internet; mutation; Signal Transduction; Software; Systems biology
Abstract

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.

DOI10.1093/nar/gkv349
Alternate JournalNucleic Acids Res.
PubMed ID25883139
PubMed Central IDPMC4489259