A flexible two-stage procedure for identifying gene sets that are differentially expressed
A flexible two-stage procedure for identifying gene sets that are differentially expressed
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DOI：
10.1093/bioinformatics/btp076
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发表时间：
2009-04-15
期刊：
影响因子：
5.8
通讯作者：
Ewens, Warren J.
中科院分区：
文献类型：
--
作者：
Heller, Ruth;Manduchi, Elisabetta;Ewens, Warren J.
动机：微阵列数据分析已从测试单个基因的差异表达扩展到测试基因组的差异表达。基因集水平的测试可以集中于多变量表达变化或基因集中至少一种基因的差异表达。这些测试在检测表达的细微变化方面可能很有效，但需要进一步检查基因集水平的发现，以了解它们是否提供信息，如果是的话，如何提供信息。结果：我们建议首先测试基因集水平的差异表达，然后继续测试已发现基因集中单个基因的差异表达。我们引入总体错误发现率（OFDR）作为测试多个基因集和基因时控制的适当错误率。我们说明了该程序相对于仅测试基因组或单个基因的程序的优势。
Motivation: Microarray data analysis has expanded from testing individual genes for differential expression to testing gene sets for differential expression. The tests at the gene set level may focus on multivariate expression changes or on the differential expression of at least one gene in the gene set. These tests may be powerful at detecting subtle changes in expression, but findings at the gene set level need to be examined further to understand whether they are informative and if so how.Results: We propose to first test for differential expression at the gene set level but then proceed to test for differential expression of individual genes within discovered gene sets. We introduce the overall false discovery rate (OFDR) as an appropriate error rate to control when testing multiple gene sets and genes. We illustrate the advantage of this procedure over procedures that only test gene sets or individual genes.