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

Clare Pacini; Francesco Iorio; Emanuel Gonçalves; Murat Iskar; Thomas Klabunde; Peer Bork; Julio Saez-Rodriguez

doi:10.1093/bioinformatics/bts656

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

Bioinformatics. 2013 Jan 1;29(1):132-4. doi: 10.1093/bioinformatics/bts656. Epub 2012 Nov 4.

Authors

Clare Pacini¹, Francesco Iorio, Emanuel Gonçalves, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Saez-Rodriguez

Affiliation

¹ European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK CB10 1SD.

Abstract

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/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Drug Repositioning*
Gene Expression Profiling
Humans
Oligonucleotide Array Sequence Analysis
Software*
Transcriptome / drug effects*