Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

We present a novel method for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles. We scan the groups of genes with a common downstream effect on the signaling network, using a mutual exclusivity criterion that ensures that each gene in the group sign...

Descripción completa

Detalles Bibliográficos
Autores principales: Babur, Özgün, Gönen, Mithat, Aksoy, Bülent Arman, Schultz, Nikolaus, Ciriello, Giovanni, Sander, Chris, Demir, Emek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381444/
https://www.ncbi.nlm.nih.gov/pubmed/25887147
http://dx.doi.org/10.1186/s13059-015-0612-6
_version_ 1782364454319554560
author Babur, Özgün
Gönen, Mithat
Aksoy, Bülent Arman
Schultz, Nikolaus
Ciriello, Giovanni
Sander, Chris
Demir, Emek
author_facet Babur, Özgün
Gönen, Mithat
Aksoy, Bülent Arman
Schultz, Nikolaus
Ciriello, Giovanni
Sander, Chris
Demir, Emek
author_sort Babur, Özgün
collection PubMed
description We present a novel method for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles. We scan the groups of genes with a common downstream effect on the signaling network, using a mutual exclusivity criterion that ensures that each gene in the group significantly contributes to the mutual exclusivity pattern. We test the method on all available TCGA cancer genomics datasets, and detect multiple previously unreported alterations that show significant mutual exclusivity and are likely to be driver events. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0612-6) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4381444
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-43814442015-04-02 Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations Babur, Özgün Gönen, Mithat Aksoy, Bülent Arman Schultz, Nikolaus Ciriello, Giovanni Sander, Chris Demir, Emek Genome Biol Method We present a novel method for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles. We scan the groups of genes with a common downstream effect on the signaling network, using a mutual exclusivity criterion that ensures that each gene in the group significantly contributes to the mutual exclusivity pattern. We test the method on all available TCGA cancer genomics datasets, and detect multiple previously unreported alterations that show significant mutual exclusivity and are likely to be driver events. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0612-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-02-26 2015 /pmc/articles/PMC4381444/ /pubmed/25887147 http://dx.doi.org/10.1186/s13059-015-0612-6 Text en © Babur et al.; licensee BioMed Central. 2015 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 use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Babur, Özgün
Gönen, Mithat
Aksoy, Bülent Arman
Schultz, Nikolaus
Ciriello, Giovanni
Sander, Chris
Demir, Emek
Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
title Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
title_full Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
title_fullStr Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
title_full_unstemmed Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
title_short Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
title_sort systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381444/
https://www.ncbi.nlm.nih.gov/pubmed/25887147
http://dx.doi.org/10.1186/s13059-015-0612-6
work_keys_str_mv AT baburozgun systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations
AT gonenmithat systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations
AT aksoybulentarman systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations
AT schultznikolaus systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations
AT ciriellogiovanni systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations
AT sanderchris systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations
AT demiremek systematicidentificationofcancerdrivingsignalingpathwaysbasedonmutualexclusivityofgenomicalterations

Ejemplares similares