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


BACKGROUND
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Salari
Keyan
K
Department of Pathology, Stanford University, Stanford, CA, USA. ksalari@stanford.edu
Tibshirani
Robert
R
Pollack
Jonathan R
JR
D056915:DNA Copy Number Variations; D018628:Gene Dosage; D015870:Gene Expression; D016678:Genome; D012984:Software