A Symmetric Length-Aware Enrichment Test

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.

• Type: Journal
• Year: 2015
• Where: RECOMB
• Authors: David Manescu, Uri Keich
• Keywords: Computational Biology, RECOMB 2015