Two great papers: Use and misuse of the gene ontology annotations <http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2363.html>. Rhee et al., (also pointed out by Pierre); http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2363.html And an overview of 14 tools performing GO enrichment analysis Ontological analysis of gene expression data: current tools, limitations, and open problems <http://bioinformatics.oxfordjournals.org/cgi/content/full/21/18/3587>. http://bioinformatics.oxfordjournals.org/cgi/content/full/21/18/3587 Klaas -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele@psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark