Figure 6.

Grh-bound loci in the embryo are associated with thousands of potential target genes that are likely regulated by Grh in specific tissues and at discrete developmental time points. (A) Venn diagrams demonstrating the overlap at three developmental time points (as indicated by color) of genes directly downregulated by Grh (left), or upregulated by Grh (right). (B) Venn diagrams divided by developmental time point showing the overlap of direct targets with those genes associated with Grh peaks identified in multiple embryonic time points. Downregulated genes are on the left, and upregulated genes are on the right. (Statistically significant P-values as calculated by Fisher’s exact test are shown.) A total of 2084 genes bound at 2–3 hr AEL, 2281 genes bound at 11–12 hr AEL, and 3342 genes bound at 15–16 hr AEL. Despite the fact that all genes that are direct targets in 2–3 hr AEL embryos and all genes that are upregulated in 11–12 hr AEL embryos are bound at multiple times over development, there is no statistically significant correlation between being bound by Grh at multiple time points and being a direct Grh target. This is because most of the genes bound at these two time points fall within these two classes. (C) Select GO term enrichment for the genes associated with the constitutively bound embryonic peaks (orange) vs. the expected number (gray). P-values are shown on the right. For a full list see Table S7.