Testing for over-representation of Gene Ontology (GO) biological processes (Harris et al., 2004; Ashburner et al., 2000) and Kyoto Encyclopedia of Genes and Genomes (KEGG) categories was performed using the Bioconductor package GOstats (Gentleman, 2004). Briefly, for each gene set tested, a list of unique Entrez-Gene identifiers was constructed. This list was then compared to the list of all known Entrez-Gene identifiers that are represented on the Affymetrix chipset Rat Genome 230 2.0. Identification of over-represented GO categories was then accomplished within GOstats using the hypergeometric distribution. GO and KEGG categories were called significant at p < 0.05.
