(1) Columbia Genome Center, Columbia University, New York, NY 10032, USA;(2) Department of Computer Science, Columbia University, New York, NY 10025, USA;(3) Department of Philosophy, University of Arizona, Tucson, AZ 85721, USA
Abstract:
Background
It is common for the results of a microarray study to be analyzed in the context of biologically-motivated groups of genes
such as pathways or Gene Ontology categories. The most common method for such analysis uses the hypergeometric distribution
(or a related technique) to look for "over-representation" of groups among genes selected as being differentially expressed
or otherwise of interest based on a gene-by-gene analysis. However, this method suffers from some limitations, and biologist-friendly
tools that implement alternatives have not been reported.