Comparison of fold changes of up- or down-regulated genes in the E11.5 rSey2/ rSey2 rat hindbrain using three analysis methods. The fold changes of the genes selected (p < 0.05) from the comparative analyses of the microarray data by GeneSpring (blue bar) and Microarray Suite (yellow bar) (shown in Additional file 1) are indicated with their real-time Q-PCR gene expression ratios (pink bar). The Q-PCR experiments were performed with LightCycler using the primers listed in Additional file 4. The genes are listed in the order of their fold change values calculated by GeneSpring. (A, A') Thirteen highly expressed genes showing high normalized signal intensity (> 1.0) in either or both conditions and high fold change value (> 2.0) in GeneSpring analyses. Since the down-regulation of Fabp7 is dramatic, the data are shown separately in (A). (B) Thirteen down-regulated genes and one up-regulated gene selected from the highly expressed genes with a fold change less than 2.0 in GeneSpring analyses. (C) Seven down-regulated genes and four up-regulated genes selected from genes showing medium normalized signal intensity (0.3-1.0) in both conditions. (D) Four down-regulated genes and two up-regulated genes with a high fold change (> 5.0), but a low expression level (normalized signal < 0.3). Groups of genes categorized in (A, A'), (B), (C) and (D) correspond to cyan, black, magenta and blue dots, respectively, in Figure 1B.