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Nucleic Acids Res. 2015 Jul 1;43(W1):W270-5. doi: 10.1093/nar/gkv349. Epub 2015 Apr 16.

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

Author information

1
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain.
2
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, 46012, Spain.
3
HPC Services, University of Cambridge, Cambridge, CB3 0RB, UK.
4
Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, 46012, Spain Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, 46012, Spain Functional Genomics Node, (INB) at CIPF, Valencia, 45012, Spain jdopazo@cipf.es.

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.

PMID:
25883139
PMCID:
PMC4489259
DOI:
10.1093/nar/gkv349
[Indexed for MEDLINE]
Free PMC Article

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