Figure 4

Characteristics of response profiles of GxE genes. (A), Left panel shows a heat map reflecting the distribution of response profiles for all GxE genes in terms of their response in the two genotypes. The right panel shows the random expectation based on marginal frequencies of different profiles in the two genotypes. (B), Twelve randomly sampled FPKM profiles for combinations of Peak and Down.late GxE profiles. Blue and red colors indicate Benning and PI 416937, respectively, as in Figure 2, where darker curves represent the mean of biological replicates shown in a lighter shade. (C), Boxplots (as in Figure 3B) showing the genotypic difference at different timpoints for GxE genes that have the same response profiles, such as Up.late in Benning and Up.late in PI 416937. ‘All’ indicates both up and down-regulated genes while ‘Up’ and ‘Down’ indicate combined sets of up and down-regulated groups. The units of the y-axis are log₂(FPKM_{PI 416937}/FPKM_Benning); positive values indicate that PI 416937 genes had higher expression than Benning at a given time-point.