Figure 2. Three broad classes of interaction effects between locus genotype and transcription factor activation affecting gene expression (for details see text).

Each marker shows the gene expression and factor activation for one individual segregant of either BY (blue) and RM (red) background at the locus, and grown in ethanol (triangles) or glucose (circles) as a carbon source. Maximum likelihood fits for expression data for the BY and RM segregants are plotted as solid lines; an interaction effect corresponds to a difference in slope in the two genetic backgrounds. (a) Genotype-environment interaction mediated by the inferred YAP1 transcription factor activation. (b) Interaction between the PHO84 locus and PHO4 transcription factor activation, which is associated both with the PHO84 locus genotype and the PHO4 probe expression level. (c) Epistatic interaction between HAP1 and its target, SCM4, mediated by the HAP1 activation.