DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.-猫眼课题宝

DOI：

10.1093/bioinformatics/btp702

发表时间：

2010-02-01

期刊：

Bioinformatics (Oxford, England)

影响因子：

通讯作者：

中科院分区：

其他

文献类型：

作者：

Salari K;Tibshirani R;Pollack JR

来源链接：

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815664/?report=classic

摘要：DNA拷贝数改变（CNA）经常是增加或减少基因剂量引起基因表达变化的基础。然而，只有一个子集的基因与改变剂量表现出一致的基因表达的变化。这个子集可能富含癌基因和肿瘤抑制基因，并且可以通过整合这两层基因组规模数据来识别。我们介绍了DNA/RNA-Integrator（DR-Integrator），一个统计软件工具，对成对的DNA拷贝数和基因表达数据进行整合分析。DR-Integrator识别DNA拷贝数和基因表达之间具有显著相关性的基因，并实施监督分析，捕获两个样本类别之间DNA拷贝数和基因表达均具有显著变化的基因。可用性：DR-Integrator可从Pollack Lab（http://pollacklab.stanford.edu/）免费获得，用于非商业用途，并可作为Microsoft Excel的插件应用程序下载，也可作为R统计计算环境的软件包下载。R包可以在http://cran.r-project.org/上以“DRI”的名称获得。使用DR-积分器的示例分析作为补充材料。联系方式：ksalari@stanford.edu; pollack1@stanford.edu补充信息：补充数据可在生物信息学在线获得。

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.