A bioinformatics method, namely Gene Set Enrichment Analysis (GSEA) (Subramanian et al. 2005), was used to detect overrepresented biochemical processes. The genes in our dataset were categorized by their Gene Ontology (GO) annotation. Briefly, the annotation file for mouse was downloaded from the GO website (www.geneontology.org) (Ashburner et al. 2000). All the sequence-verified genes included in the chip were searched against this annotation, and the biological process, molecular function, and cellular component categories of each gene were extracted. Each gene was assigned to one or more GO categories, and several highly related categories were combined because only a few genes were represented in each process. The constructed gene sets and the gene expression data were loaded into GSEA to detect enriched GO categories.
