Journal Article

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data

Keyan Salari, Robert Tibshirani and Jonathan R. Pollack

in Bioinformatics

Volume 26, issue 3, pages 414-416
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp702

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Summary: DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage. However, only a subset of genes with altered dosage exhibit concordant changes in gene expression. This subset is likely to be enriched for oncogenes and tumor suppressor genes, and can be identified by integrating these two layers of genome-scale data. We introduce DNA/RNA-Integrator (DR-Integrator), a statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between DNA copy number and gene expression, and implements a supervised analysis that captures genes with significant alterations in both DNA copy number and gene expression between two sample classes.

Availability: DR-Integrator is freely available for non-commercial use from the Pollack Lab at http://pollacklab.stanford.edu/ and can be downloaded as a plug-in application to Microsoft Excel and as a package for the R statistical computing environment. The R package is available under the name ‘DRI’ at http://cran.r-project.org/. An example analysis using DR-Integrator is included as supplemental material.

Contact: ksalari@stanford.edu; pollack1@stanford.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1422 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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