A statistical framework for testing functional categories in microarray data
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Publication:2482980
Abstract: Ready access to emerging databases of gene annotation and functional pathways has shifted assessments of differential expression in DNA microarray studies from single genes to groups of genes with shared biological function. This paper takes a critical look at existing methods for assessing the differential expression of a group of genes (functional category), and provides some suggestions for improved performance. We begin by presenting a general framework, in which the set of genes in a functional category is compared to the complementary set of genes on the array. The framework includes tests for overrepresentation of a category within a list of significant genes, and methods that consider continuous measures of differential expression. Existing tests are divided into two classes. Class 1 tests assume gene-specific measures of differential expression are independent, despite overwhelming evidence of positive correlation. Analytic and simulated results are presented that demonstrate Class 1 tests are strongly anti-conservative in practice. Class 2 tests account for gene correlation, typically through array permutation that by construction has proper Type I error control for the induced null. However, both Class 1 and Class 2 tests use a null hypothesis that all genes have the same degree of differential expression. We introduce a more sensible and general (Class 3) null under which the profile of differential expression is the same within the category and complement. Under this broader null, Class 2 tests are shown to be conservative. We propose standard bootstrap methods for testing against the Class 3 null and demonstrate they provide valid Type I error control and more power than array permutation in simulated datasets and real microarray experiments.
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- A statistical framework for testing functional categories in microarray data
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Cited in
(10)- An empirical Bayesian approach for identifying differential coexpression in high-throughput experiments
- Pathway analysis for RNA-seq data using a score-based approach
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- Accounting for extra-binomial variability with differentially expressed genetic pathway data: a collaborative bioinformatic study
- A statistical framework for testing functional categories in microarray data
- Multiple tests of association with biological annotation metadata
- Statistical and knowledge supported visualization of multivariate data
- A high-dimensional two-sample test for the mean using random subspaces
- Test-statistic correlation and data-row correlation
- Analyzing time-course microarray data using functional data analysis -- a review
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