Fig. 4

Comparative analysis reveals 112 concordant Shh-regulated genes. a Schematic of in vitro Shh pathway activation of cNCCs. b Schematic of in vivo Shh pathway inhibition by cyclopamine. Red shading marks cNCCs that would normally respond to SHH ligand stimulation but are blocked by cyclopamine. c Comparison of the significant differentially expressed genes between the in vitro model of Shh pathway activation (2749 genes) and the in vivo model of Shh-pathway inhibition (1039 genes). 178 differentially expressed genes are common and overlap between the two microarrays. d Scatter plot of 178 common genes. Y-axis shows fold change (SHH/Veh) for the in vitro model of Shh pathway activation, while the X-axis shows fold change (Veh/Cyc) for the in vivo model of Shh pathway inhibition. For clarity of results, in vivo fold change is plotted as Veh/Cyc, such that positively regulated Shh targets appear upregulated in the array and negatively regulated Shh targets appear downregulated. 43 genes show concordant upregulation (positive regulation by Shh signaling, yellow), and 69 genes show concordant downregulation (negatively regulated by Shh signaling, blue). The bona fide Shh targets Gli1 and Gas1 are highlighted. Known orofacial cleft (OFC)-associated genes, including Gas1, are marked by magenta X’s [15]. e The top 30 concordant up- and downregulated genes are listed by rank sum, with OFC-associated genes in magenta. See Table 1 and Table 2 for specific fold changes and FDR p-values and Additional files 5 and 6 for gene ranking. A full list of the 112 concordant Shh-regulated genes and the 67 genes with non-concordant changes with their respective linear fold changes can be found in Additional file 4. In vivo array utilized stage-matched FNP tissue from n = 6 vehicle and n = 6 cyclopamine-exposed pooled litters