Quantitative RT-PCR analysis of gene expression in E13.5 Pax9−/− palatal shelves. The mRNA levels of a select group of differentially expressed genes were verified in microdissected palatal shelves of Pax9+/+ and Pax9−/− mouse embryos by quantitative RT-PCR (n=5 per group). Pax9 deficiency affects the expression of Wnt signaling pathway genes and known partner genes of Pax9. The expression levels of Dkk1 and Dkk2 are significantly upregulated in the absence of Pax9. By contrast, Wnt signaling pathway downstream targets, such as Lef1, Gbx2, Fgf4 and Hand2, as well as the Pax9 partner genes Msx1 and Msx2, were significantly downregulated in Pax9−/− samples. Results are shown as percentage of the mean±s.e.m. of the Pax9+/+ group. *P<0.01.