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DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E,
Iskar M, Klabunde T,
Bork P, Saez-Rodriguez J
Bioinformatics.
2013 Jan 1; 29(1): 132-4. Epub 2012 Nov 4; PubMed:
23129297.Abstract + PDF
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 whilst 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, GEO 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: Accompanies this paper.