Estimates of gene expression levels for three yeast transcription factors after 30 minutes of exposure to 7% vol/vol ethanol during peak growth phase. (a) Likelihood contour plots for the relative gene-expression level () and experimental error variance (2). For each gene, surfaces have a single peak. (b) Credible intervals for gene-expression level for three yeast transcription factors that are candidates for the ethanol shock response, taken from cultures at log-phase growth either unexposed or exposed to 30 min of 7% v/v ethanol. Because the slope of the likelihood is much steeper to the right than to the left of this ridge represented in (a), credible intervals with two-sample data such as this are highly asymmetric. More balanced experimental designs have more symmetric credible intervals. Using a conservative gene-by-gene criterion of nonoverlapping 95% credible intervals, none of these transcription factors shows statistically significantly differential gene expression, although GCR1 is close. MSN4 is the gene for a zinc-finger transcriptional activator for genes regulated through Snf1p. A general regulator for stress response, it does not seem to be responsible for upregulation of stress genes in response to ethanol. HSF1 is the gene for a heat-shock transcription factor that binds to the heat-shock DNA element at both normal and elevated temperatures. Although the difference in estimates observed here is suggestive of regulatory action of the heat-shock response, these differences are not statistically significant. GCR1 encodes a positive regulator of glycolytic genes, including GLK1. Although the difference in estimates observed here is suggestive of regulatory action on transcription of transposable elements and the trehalose pathway, the differences are not statistically significant by a conservative criterion of nonoverlapping 95% credible intervals.
Townsend and Hartl Genome Biology 2002 3:research0071.1 doi:10.1186/gb-2002-3-12-research0071