Epistasis between genomic and environmental perturbations. A. Schematic illustration of epistasis and additivity. The environmentally and genetically induced transcriptional changes are defined as ΔTE and ΔTG, respectively. When genetic and environmental perturbations occurred together, the simultaneous change in expression is defined as ΔTF. 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, ΔTE + ΔTG) is plotted against the transcriptional changes caused simultaneously by both perturbations (the simultaneous contribution, ΔTF), 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.
Ying et al. BMC Genomics 2013 14:25 doi:10.1186/1471-2164-14-25