Not necessary, but might add if reviewers insist: Table S5: lists of genes within each interacting pair

The dawn gene expression waves are delayed in both phyAphyBcry1cry2 (red and blue light signalling) and prr5prr7prr9 (circadian) mutants

DNA binding proteins appear to have multiple coordinated bursts of expression at dawn and these bursts are either light or temperature dependent or both.  To characterise the gene regulatory mechanisms that underly these changes, we performed RNA-seq on a series of mutant strains that perturbed red- and blue-light sensitivity (phyAphyBcry1cry2 , Ler background), the circadian clock (prr5prr7prr9, Col-0 background) and temperature sensitivity (hsfA1Q, Col-0 background ), all of which have all been previously characterised (Yanovsky, Mazzella, and Casal 2000; Liu et al. 2013; Yoshida et al. 2011) .  These were sampled at the most informative time points according to NITPicker (CITE) .   We are able to see the same patterns of expression in this subset of  time points as we were able to see in the original time series in Col-0 (Figure 2C ).     We observe that the genes within each of these clusters have perturbed patterns of expression in the mutant strains (Figure 2C ).  The gene expression appears to be delayed in both prr5prr7prr9 and phyAphyBcry1cry2.  In particular, the early expressing genes were up-regulated in both the prr5prr7prr9 and phyAphyBcry1cry2 mutants and were expressed for a larger portion of the time series, while the late expressing genes appeared later in the time series.
Additionally, clusters 5-6 (which include many light responsive genes) are expressed later in the time series (at 105-120 minutes instead of 45-60 minutes) in the prr5prr7prr9 and phyAphyBcry1cry2 mutants and at higher expression levels.    Clusters 7-8 (which include HSF1A1 and was expressed at higher levels in elevated temperature) was found to have higher expression levels in hsf1aQ, prr5prr7prr9, and phyAphyBcry1cry2 compared to Col-0 and Ler.  Finally, the gene expression within clusters 9-10 was less coordinated in the mutants than the WT and there wasn’t as consistent a pattern of up- or down-regulation.
So far, our analysis has focussed on genes encoding DNA binding proteins.  However, many of these DNA binding proteins encode for transcription factors that may regulate downstream targets.  We wished to identify modules of genes that behaved similarly to one another across at least three conditions, as these sets of genes might be regulated by the same set of genes.  To do this, we performed clustering separately for every condition and then identified pairs of genes that were part of the same cluster under four of the five conditions (see Figure S3 ).  All genes that were in at least one such pair were selected for further analysis (see Figure S4 ).