Enrichment analysis of functional groups of up- and down-regulated genes associated with chronic glutamate hyperactivity. (A) Approximately 2% of the over 39,000 gene transcripts surveyed by Affymetrix Mouse Genome 430 2.0 Array were identified to be significantly up-regulated, and 1% to be down-regulated, with an FDR of 0.9%. (B, C) Gene Ontology (GO) analysis of up- (B) and down-regulated (C) biological processes associated with chronic glutamate hyperactivity. This analysis was conducted with GO-elite using hypergeometric distribution. A Z score > 1.96 or < -1.96 and a permute P value < 0.05, were considered to be statistically significant. (D, E) Comparative analyses of over-represented bio-functions and canonical pathways, respectively, in up- and down-regulated genes using Ingenuity Pathway Analysis (IPA). Significance calculated by IPA was plotted as -log P value and the dashed line corresponds to the threshold P = 0.05.