Department of Pathology, Stanford University, Stanford, CA, USA.
Bioinformatics. 2010 Feb 1;26(3):414-6. doi: 10.1093/bioinformatics/btp702. Epub 2009 Dec 22.
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.
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.
Supplementary data are available at Bioinformatics online.
DNA 拷贝数改变（CNA）通过增加或减少基因剂量经常导致基因表达的变化。然而，只有改变剂量的一小部分基因表现出基因表达的一致变化。这个亚组可能富含癌基因和肿瘤抑制基因，可以通过整合这两层基因组规模的数据来识别。我们引入了 DNA/RNA 整合器（DR-Integrator），这是一种统计软件工具，用于对配对的 DNA 拷贝数和基因表达数据进行综合分析。DR-Integrator 确定了 DNA 拷贝数和基因表达之间存在显著相关性的基因，并实施了一种监督分析，该分析捕获了在两个样本类之间的 DNA 拷贝数和基因表达都发生显著改变的基因。
DR-Integrator 可免费用于非商业用途，可从斯坦福大学 Pollack 实验室的 http://pollacklab.stanford.edu/ 获得，并可作为 Microsoft Excel 的插件应用程序和 R 统计计算环境的软件包下载。R 软件包的名称为“DRI”，可在 http://cran.r-project.org/ 获得。使用 DR-Integrator 的示例分析包含在补充材料中。
补充数据可在生物信息学在线获得。
