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Figure 6 | Genome Biology

Figure 6

From: Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments

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.

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