DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

Summary: Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively cor...

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Detalles Bibliográficos
Autores principales: Pacini, Clare, Iorio, Francesco, Gonçalves, Emanuel, Iskar, Murat, Klabunde, Thomas, Bork, Peer, Saez-Rodriguez, Julio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530913/
https://www.ncbi.nlm.nih.gov/pubmed/23129297
http://dx.doi.org/10.1093/bioinformatics/bts656
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author Pacini, Clare
Iorio, Francesco
Gonçalves, Emanuel
Iskar, Murat
Klabunde, Thomas
Bork, Peer
Saez-Rodriguez, Julio
author_facet Pacini, Clare
Iorio, Francesco
Gonçalves, Emanuel
Iskar, Murat
Klabunde, Thomas
Bork, Peer
Saez-Rodriguez, Julio
author_sort Pacini, Clare
collection PubMed
description Summary: Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively correlated profiles may be used to infer side effects of drugs. DvD allows users to compare drug and disease signatures with dynamic access to databases Array Express, Gene Expression Omnibus and data from the Connectivity Map. Availability and implementation: R package (submitted to Bioconductor) under GPL 3 and Cytoscape plug-in freely available for download at www.ebi.ac.uk/saezrodriguez/DVD/. Contact: saezrodriguez@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-35309132012-12-27 DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data Pacini, Clare Iorio, Francesco Gonçalves, Emanuel Iskar, Murat Klabunde, Thomas Bork, Peer Saez-Rodriguez, Julio Bioinformatics Applications Note Summary: Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively correlated profiles may be used to infer side effects of drugs. DvD allows users to compare drug and disease signatures with dynamic access to databases Array Express, Gene Expression Omnibus and data from the Connectivity Map. Availability and implementation: R package (submitted to Bioconductor) under GPL 3 and Cytoscape plug-in freely available for download at www.ebi.ac.uk/saezrodriguez/DVD/. Contact: saezrodriguez@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2013-01 2012-11-04 /pmc/articles/PMC3530913/ /pubmed/23129297 http://dx.doi.org/10.1093/bioinformatics/bts656 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Pacini, Clare
Iorio, Francesco
Gonçalves, Emanuel
Iskar, Murat
Klabunde, Thomas
Bork, Peer
Saez-Rodriguez, Julio
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
title DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
title_full DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
title_fullStr DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
title_full_unstemmed DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
title_short DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
title_sort dvd: an r/cytoscape pipeline for drug repurposing using public repositories of gene expression data
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530913/
https://www.ncbi.nlm.nih.gov/pubmed/23129297
http://dx.doi.org/10.1093/bioinformatics/bts656
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