PTCH1 and omphalocele: Further DE gene analysis in Cluster 1 showed that Pitx2 is significantly upregulated (Log2FC 1.05, adjusted P=2.1×10−11) and Ptch1, a component of the Shh pathway that is associated with omphalocele (Matsumaru et al., 2011), is significantly downregulated (Log2FC −1.86, adjusted P=9.45×10−7; Table S8).