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A Symmetric Length-Aware Enrichment Test

  • David Manescu
  • Uri KeichEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9029)

Abstract

Young et al. [14] showed that due to gene length bias the popular Fisher Exact Test should not be used to study the association between a group of differentially expressed (DE) genes and a specific Gene Ontology (GO) category. Instead they suggest a test where one conditions on the genes in the GO category and draws the pseudo DE expressed genes according to a length-dependent distribution. The same model was presented in a different context by Kazemian et al. who went on to offer a dynamic programming (DP) algorithm to exactly estimate the significance of the proposed test [8]. Here we point out that while valid, the test proposed by these authors is no longer symmetric as Fisher’s Exact Test is: one gets different answers if one conditions on the observed GO category than on the DE set. As an alternative we offer a symmetric generalization of Fisher’s Exact Test and provide efficient algorithms to evaluate its significance.

Keywords

Gene Ontology Monte Carlo Conditional Moment Saddlepoint Approximation Probability Weighting Function 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.School of Mathematics and StatisticsUniversity of SydneySydneyAustralia

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