Testing for over-representation of GO (Harris et al., 2004; Ashburner et al., 2000) biological processes (BP) and molecular function (MF) 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. Only categories with greater than 9 and less than 300 genes represented on the chipset were included in the analysis; only categories with more than 5 significant genes are listed. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) categories were called significant at p < 0.05. Curated pathway analyses on significant genes were conducted with Ingenuity® Pathways Analyses.
