Cargando…
Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples
BACKGROUND: Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platform...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001047/ https://www.ncbi.nlm.nih.gov/pubmed/29898651 http://dx.doi.org/10.1186/s12859-018-2234-y |
_version_ | 1783331899134967808 |
---|---|
author | Díaz-Gay, Marcos Vila-Casadesús, Maria Franch-Expósito, Sebastià Hernández-Illán, Eva Lozano, Juan José Castellví-Bel, Sergi |
author_facet | Díaz-Gay, Marcos Vila-Casadesús, Maria Franch-Expósito, Sebastià Hernández-Illán, Eva Lozano, Juan José Castellví-Bel, Sergi |
author_sort | Díaz-Gay, Marcos |
collection | PubMed |
description | BACKGROUND: Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts. RESULTS: In this work we present Mutational Signatures in Cancer (MuSiCa), a new web tool based on MutationalPatterns and built using the Shiny framework in R language. By means of a simple interface suited to non-specialized researchers, it provides a comprehensive analysis of the somatic mutational status of the supplied cancer samples. It permits characterizing the profile and burden of mutations, as well as quantifying COSMIC-reported mutational signatures. It also allows classifying samples according to the above signature contributions. CONCLUSIONS: MuSiCa is a helpful web application to characterize mutational signatures in cancer samples. It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2234-y) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6001047 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60010472018-06-26 Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples Díaz-Gay, Marcos Vila-Casadesús, Maria Franch-Expósito, Sebastià Hernández-Illán, Eva Lozano, Juan José Castellví-Bel, Sergi BMC Bioinformatics Software BACKGROUND: Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic packages to address this topic have been developed in different languages/platforms. MutationalPatterns has arisen as the most efficient tool for the comparison with the signatures currently reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. However, the analysis of mutational signatures is nowadays restricted to a small community of bioinformatic experts. RESULTS: In this work we present Mutational Signatures in Cancer (MuSiCa), a new web tool based on MutationalPatterns and built using the Shiny framework in R language. By means of a simple interface suited to non-specialized researchers, it provides a comprehensive analysis of the somatic mutational status of the supplied cancer samples. It permits characterizing the profile and burden of mutations, as well as quantifying COSMIC-reported mutational signatures. It also allows classifying samples according to the above signature contributions. CONCLUSIONS: MuSiCa is a helpful web application to characterize mutational signatures in cancer samples. It is accessible online at http://bioinfo.ciberehd.org/GPtoCRC/en/tools.html and source code is freely available at https://github.com/marcos-diazg/musica. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2234-y) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-14 /pmc/articles/PMC6001047/ /pubmed/29898651 http://dx.doi.org/10.1186/s12859-018-2234-y Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 | Software Díaz-Gay, Marcos Vila-Casadesús, Maria Franch-Expósito, Sebastià Hernández-Illán, Eva Lozano, Juan José Castellví-Bel, Sergi Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
title | Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
title_full | Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
title_fullStr | Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
title_full_unstemmed | Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
title_short | Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples |
title_sort | mutational signatures in cancer (musica): a web application to implement mutational signatures analysis in cancer samples |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001047/ https://www.ncbi.nlm.nih.gov/pubmed/29898651 http://dx.doi.org/10.1186/s12859-018-2234-y |
work_keys_str_mv | AT diazgaymarcos mutationalsignaturesincancermusicaawebapplicationtoimplementmutationalsignaturesanalysisincancersamples AT vilacasadesusmaria mutationalsignaturesincancermusicaawebapplicationtoimplementmutationalsignaturesanalysisincancersamples AT franchexpositosebastia mutationalsignaturesincancermusicaawebapplicationtoimplementmutationalsignaturesanalysisincancersamples AT hernandezillaneva mutationalsignaturesincancermusicaawebapplicationtoimplementmutationalsignaturesanalysisincancersamples AT lozanojuanjose mutationalsignaturesincancermusicaawebapplicationtoimplementmutationalsignaturesanalysisincancersamples AT castellvibelsergi mutationalsignaturesincancermusicaawebapplicationtoimplementmutationalsignaturesanalysisincancersamples |