CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies

SUMMARY: Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. How...

Full description

Bibliographic Details
Authors: Hernandez-Ferrer, Carles, 1987-, González Ruiz, Juan Ramón
Format: article
Status:Published version
Publication Date:2018
Country:España
Institution:Universitat Pompeu Fabra
Repository:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/34979
Online Access:http://hdl.handle.net/10230/34979
http://dx.doi.org/10.1093/bioinformatics/bty326
Access Level:Open access
Keyword:Genòmica
Medi ambient
Malalties
Programari
id ES_c9b61c26547b3b962b0e7686876fc486
oai_identifier_str oai:repositori.upf.edu:10230/34979
network_acronym_str ES
network_name_str España
repository_id_str
spelling CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studiesHernandez-Ferrer, Carles, 1987-González Ruiz, Juan RamónGenòmicaMedi ambientMalaltiesProgramariSUMMARY: Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. However, there is a need to perform similar analyses at the chemicals-genes or chemicals-diseases levels, to provide complementary knowledge of the causal path between chemicals and diseases. While the Comparative Toxicogenomics DatabaseTM (CTD) provides information about these relationships, there is no software for integrating it into R/Bioconductor analysis pipelines. CTDquerier helps users to easily download CTD data and integrate it in the R/Bioconductor framework. The package also contains functions for visualizing CTD data and performing enrichment analyses. We illustrate how to use the package with a real data analysis of asthma-related genes. CTDquerier is a flexible and easy-to-use Bioconductor package that provides novel hypothesis about the relationships between chemicals and diseases. AVAILABILITY AND IMPLEMENTATION: CTDquerier R package is available through Bioconductor and its development version at https://github.com/isglobal-brge/CTDquerier.This work was supported by the Spanish Ministry of Economy and Competitiveness [MTM2015-68140-R] and the HELIX Project supported by European Commission FP7 [GA#308333]. C.H.F. is supported by funding from the National Institutes of Mental Health [NIMH R01MH107205]Oxford University Press201820182018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/34979http://dx.doi.org/10.1093/bioinformatics/bty326reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésBioinformatics. 2018 Sep 15;34(18):3235-7info:eu-repo/grantAgreement/EC/FP7/308333info:eu-repo/grantAgreement/ES/1PE/MTM2015-68140-R© Carles Hernandez-Ferrer, Juan R Gonzalez 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution Licensehttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/349792026-06-12T07:21:37Z
dc.title.none.fl_str_mv CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
spellingShingle CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
Hernandez-Ferrer, Carles, 1987-
Genòmica
Medi ambient
Malalties
Programari
title_short CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_full CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_fullStr CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_full_unstemmed CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
title_sort CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
dc.creator.none.fl_str_mv Hernandez-Ferrer, Carles, 1987-
González Ruiz, Juan Ramón
author Hernandez-Ferrer, Carles, 1987-
author_facet Hernandez-Ferrer, Carles, 1987-
González Ruiz, Juan Ramón
author_role author
author2 González Ruiz, Juan Ramón
author2_role author
dc.subject.none.fl_str_mv Genòmica
Medi ambient
Malalties
Programari
topic Genòmica
Medi ambient
Malalties
Programari
description SUMMARY: Biomedical studies currently include a large volume of genomic and environmental factors for studying the etiology of human diseases. R/Bioconductor projects provide several tools for performing enrichment analysis at gene-pathway level, allowing researchers to develop novel hypotheses. However, there is a need to perform similar analyses at the chemicals-genes or chemicals-diseases levels, to provide complementary knowledge of the causal path between chemicals and diseases. While the Comparative Toxicogenomics DatabaseTM (CTD) provides information about these relationships, there is no software for integrating it into R/Bioconductor analysis pipelines. CTDquerier helps users to easily download CTD data and integrate it in the R/Bioconductor framework. The package also contains functions for visualizing CTD data and performing enrichment analyses. We illustrate how to use the package with a real data analysis of asthma-related genes. CTDquerier is a flexible and easy-to-use Bioconductor package that provides novel hypothesis about the relationships between chemicals and diseases. AVAILABILITY AND IMPLEMENTATION: CTDquerier R package is available through Bioconductor and its development version at https://github.com/isglobal-brge/CTDquerier.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/34979
http://dx.doi.org/10.1093/bioinformatics/bty326
url http://hdl.handle.net/10230/34979
http://dx.doi.org/10.1093/bioinformatics/bty326
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Bioinformatics. 2018 Sep 15;34(18):3235-7
info:eu-repo/grantAgreement/EC/FP7/308333
info:eu-repo/grantAgreement/ES/1PE/MTM2015-68140-R
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869419394624389120
score 15,81155

Similar Items