Figure 3: Analysis of higher confidence morning gene network.  (A) This depicts the complete network of gene regulatory relationships that are predicted by dynGenie3 and consistent with DAP-seq data.  All genes that regulate at least one downstream target are coloured dark blue, while other genes are colour-coded by the time period in which they have maximal expression (as expressed as the average gene expression in 3 adjacent time points).  (B) This graph depicts enrichment for pairs of GO terms within the network, as determined by the PAFway package.  The specific upstream and downstream targets predicted for HY5 (C) and BBX31 (D) are shown.   Genes that are discussed in the text are highlighted in bold for clarity.  The colour key is the same as in (A).