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. 2008 Oct 1;22(19):2651–2663. doi: 10.1101/gad.1693008

Figure 3.

Figure 3.

(A) A range of Shh pathway genotypes were assayed for gene expression at E11.5, as well as limb buds dissected into anterior (Ant) and posterior (Post) compartments to define Hh-nonresponsive and Hh-responsive compartments, respectively. Gene expression indices derived from exon arrays were used in several pairwise combinations as well as multivariable combinations. The criteria shown in the heat map are Ant < Post and Shh < wild type < SmoM2 and Gli3 > SmoGli3 with an FDR < 10% and posterior probability cutoff of <25%. (B) By associating 753 genes differentially expressed in these conditions with GBRs (FDR < 50%), we are able to assign binding regions putative target genes. We obtain 656 binding regions, including 396 that contain Gli motifs; these are associated with 205 genes. (C–J) Examples of binding regions (∼500 kb) and the associated differentially expressed genes. The coordinates (mm8) are shown above each graph, while Ref_Seq transcripts are shown below. Genes and transcripts in red indicate differentially expressed genes.