!Citation=Smith EN, Kruglyak L (2008) PLoS Biol 6(4): e83 doi:10.1371/journal.pbio.0060083 !Title=Gene-Environment Interaction in Yeast Gene Expression !PubMedID= !Name=BYxRM glucose and ethanol !ExptSetNo=5446 !Description=This experiment set contains arrays from a quantitative trait locus (QTL) mapping study that was performed in two conditions (glucose and ethanol carbon sources). There are 6 biological replicates of each parent (BY4716 and RM11-1a) grown in each condition. There are also 109 segregants from a cross between BY4716 and RM11-1a that have each been grown in each condition. Finally, there are 2 replacement strains that carry a portion of one parent's genome in the other parent's background (YLK807 = BY4724 + IRA2-RM, YLK810 = RM11-1a + IRA2-BY). Genetic variants influence traits, but their effects can be dependent on environmental and physiological conditions. We sought to understand how this gene-environment interaction works on a molecular level by studying the genetic and molecular basis of variation in gene expression between two yeast strains (BY and RM) grown in two different conditions (glucose and ethanol carbon sources). When we examined these strains, we observed that most transcripts vary by strain and condition, with 2996, 3448, and 2037 transcripts showing significant strain, condition, and strain-condition interaction effects, respectively. Using a collection of segregants derived from a cross between BY and RM, we characterized 1555 linkages for 1382 transcripts that show significant gene-environment interaction. At the locus level, local linkages tend to be more stable across conditions, such that they are more likely show the same effect or the same direction of effect across conditions. Distant linkages are more condition-dependent, and often show effects in different directions in the two conditions. We characterized a locus that influences expression of ribosome biogenesis and energy-metabolism related transcripts, and showed that polymorphism in IRA2 is a major contributor to the variation. Furthermore, the RM allele of IRA2 appears to be more functional than the BY allele across these conditions. This dataset provides a rich resource...