Epistasis between genomic and environmental perturbations. A. Schematic illustration of epistasis and additivity. The environmentally and genetically induced transcriptional changes are defined as ΔT
, respectively. When genetic and environmental perturbations occurred together, the simultaneous change in expression is defined as ΔT
. The relationships among these three parameters were described with the indicated equations, where α represents the magnitude of the epistatic effect. B. Antagonistic epistasis in the transcriptome. The sum of the transcriptional changes caused separately by genetic and environmental perturbations (the additive contribution, ΔT
) is plotted against the transcriptional changes caused simultaneously by both perturbations (the simultaneous contribution, ΔT
), i.e., the changes in gene expression between MDS42_heatshock and MG1655. The 3710 common genes and the genes showing significant fluctuations induced by either genetic or environmental perturbation (both DEGs_gr and DEGs_hs) are plotted in the upper and bottom panels, respectively. The values of α were calculated as follows: α = 1 – k, where k is the slope of the dot plot fit by linear regression, as indicated by the solid black line.