The set of candidate effectors or upstream activators of Hox-mediated patterning. (A) A summary of expression profiles (r2–r5) of the genes identified by ANOVA (p = 0.05). Each line represents the expression of one gene where 1 is equivalent to the median of each gene's expression across the experiment. Therefore, >1 predicts enriched expression whereas <1 suggests reduced expression relative to the median. Normalised values for each gene represented are detailed in Additional file 3. (B) GeneChip expression profiles of the hindbrain patterning genes are concordant with the endogenous expression domains. Subtleties in the expression values can also be detected. For example, Hoxa2 expression is elevated in r3 and r5 and this is consistent with its known transcriptional activation in this region by Egr2. Together, these data show that the methods used here generate a faithful depiction of known gene expression across the hindbrain. At E9.5, Egr2, the primary determinant of r3 and r5 territories, is expressed only in r5 (Figure 4A'-A"'). The expression of some of the known Hox/Egr2 downstream targets (for example, Nab1/2) is accurately represented. Data represented as mean normalised value +/- SEM.