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brain-map.org/, Lein et al. 2007; Glattfelder et al. 2008) with our transcriptome catalogues in the SD (S2) and WKY rat (S3). We find excellent correlation between rat and mouse AP gene expression; of the 50 genes whose expression has been mapped in the mouse AP, 42 are represented on the rat chip, of which 37 (88%) are flagged as Present in at least one of our experimental groups (the majority in all five groups; S10). In order to investigate strain differences between the inbred WKY rat and the outbred SD rat, we compiled a new list that combined the SD (S2) and WKY (S3) Present lists. We filtered this new check details list for those genes that are significantly different between these two strains (Welch t-test B&H, P diglyceride the WKY AP compared with the SD. The majority of the genes in the AP are, however, well conserved between the two strains; 13,911 genes (data not shown) are considered to be Present in both the SD and the WKY AP. Comprehensive catalogues of AP gene expression. The sensory function of the AP led us to focus on specific broad groups of genes whose expression within the SD or WKY AP directly contributes to this function, namely receptors (including G protein-coupled receptors; GPCRs) and ion channels. Lists of genes that are represented on the Affymetrix array were isolated using the wildcard operator terms ��receptor�� (1409), ��GPCR��, ��GPR�� and ��G protein-coupled receptor�� (324) or ��channel�� (300). When we compared the lists of putative receptors with the SD + WKY list, we identified a population of 579 receptors in the AP of either the SD or the WKY (or both), of which 107 were identified as GPCRs (S7; Fig. 2). Comparison of the channel list IOX1 revealed 108 genes annotated as ��channel�� in their gene title or symbol (S8; Fig. 3). We have also selected signalling molecules that may act as ligands for these receptors and whose expression in the AP has previously been demonstrated (Fig. 2). Steady-state changes in transcriptome expression. We applied statistical testing (Welch ANOVA + Tukey post hoc test and B&H, P > 0.05) to our SD + FSD + DSD + WKY + SHR Present list. Following a 1.5-fold cut-off, 53 genes in the DSD AP (S13) and 29 genes in the FSD AP (S13) were regulated compared with the SD AP (Fig. 1). In the SHR AP (S14), 315 genes were regulated compared with the WKY AP. Filtering of this list revealed four genes that converge on known rat quantitative trait loci (QTL; Fig. 4), and GO analysis (P