Scatter plots of gene expression levels in the hindbrain of E11.5 rSey2/ rSey2 and WT rat embryos. (A) Average per chip normalized signal intensities for all probe sets on GeneChip 230A and 230B are plotted using GeneSpring software. The dots are colored according to their per gene normalized values for rSey2/rSey2 (vertical) compared to WT (horizontal): high (red), equal (yellow) and low (green). The reliability of the data is indicated by a dark-light gradient; genes with higher confidence are deeper in color. The three blue lines correspond to 2-fold up-regulation (+2), no change (± 1) and 2-fold down-regulation (-2) for rSey2/rSey2 compared to WT. (B) The 1,421 differentially expressed genes selected by t-test using the cross-gene error model (p < 0.05). Gray and brown lines indicate the normalized signal as 1 and 0.3, respectively. Cyan, black, magenta and blue dots with gene names correspond to the probe sets that are listed in Additional file 4 and displayed in Figure 3. The colors of the dots reflect expression levels and fold change values: cyan, high expression (normalized signal > 1) with more than a 2-fold change; black, high expression with less than a 2-fold change; magenta, medium expression (normalized signal 0.3 to 1); and blue, low expression (normalized signal < 0.3) with more than a 5-fold change. The seven probe sets indicated with arrows correspond to four of the most down-regulated genes, which are shown in situ in Figures 4 and 5.