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BMC Bioinformatics BioMed Central Software Open Access CoXpress: differential co-expression in gene expression data Michael Watson*† Address: Informatics Group, Institute for Animal Health, Compton, Newbury, Berks RG20 7NN, UK Email: Michael Watson* - michael.watson@bbsrc.ac.uk * Corresponding author †Equal contributors Published: 20 November 2006 Received: 21 July 2006 Accepted: 20 November 2006 BMC Bioinformatics 2006, 7:509 doi:10.1186/1471-2105-7-509 This article is available from: /1471-2105/7/509 © 2006 Watson; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Traditional methods of analysing gene expression data often include a statistical test to find differentially expressed genes, or use of a clustering algorithm to find groups of genes that behave similarly across a dataset. However, these methods may miss groups of genes which form differential co-expression patterns under different subsets of experimental conditions. Here we describe coXpress, an R package that allows researchers to identify groups of genes that are differentially co-expressed. Results: We have developed coXpress as a means of identifying groups of genes that are