Figure 6.

Statistical and biological significance of inferred gene expression levels in swi1Δ, snf2Δ, and zap1 mutants compared to wild type (WT). (a) Scatterplot of the log2 BAGEL estimate of fold-change in the swi1Δ mutant compared to wild type for all genes (on the x-axis) versus the negative overlap of BAGEL credible intervals for the swi1Δ mutant compared to wild type. Points above zero on the y-axis have nonoverlapping 95% credible intervals. Dashed lines indicate a twofold difference in estimate of gene-expression level. Points outside the region defined by these dashed lines and below zero on the y-axis have low statistical significance despite their high estimated fold-change. Points within the region defined by these dashed lines and above zero on the y-axis have high statistical significance and a low fold-change. Note that these points are very densely packed and appear close to zero on the y-axis because the difference between confidence intervals cannot exceed the difference between estimates. (b) Scatterplot of log2 fold-change of gene-expression levels in the swi1Δ mutant compared to wild type against gene-expression levels of the snf2Δ mutant. Genes shown have nonoverlapping 95% credible intervals with wild type. The regression passes through zero without forcing. (c) Scatterplot of the log2 BAGEL estimate of fold-change in the zap1 mutant in zinc-deficient medium compared to wild type in zinc-deficient medium for all genes (on the x-axis) versus the negative overlap of BAGEL credible intervals for the zap1 mutant compared to wild type in zinc-deficient medium. (d) Scatterplot of log2 fold-change of gene-expression levels in zap1 mutant compared to wild type in zinc-deficient medium versus wild type in zinc-replete medium compared to wild type in zinc-deficient medium. The regression is forced through zero; its y-intercept and slope are slightly lower when not forced. Genes shown have nonoverlapping 95% credible intervals with wild type.

Townsend and Hartl Genome Biology 2002 3:research0071.1-research0071.16   doi:10.1186/gb-2002-3-12-research0071