Figure 1

Experimental designs for three studies analyzed using the BAGEL framework. Each circle represents an expression 'node', typically characterized by a particular genotype, environment and developmental state. Here, each circle is inscribed with a genotype and environment. Arrows represent individual two-color cDNA microarray experiments, with the arrowhead pointing toward the sample labeled with the Cy3 fluorophore. (a) A comparison of global gene expression of wild-type (WT) yeast in rich medium at log-growth to that of yeast at log-growth after 30 min exposure to 7% v/v ethanol [11]. (b) A comparison of swi1Δ and snf2Δ mutants to wild type in rich and minimal media [12]. (c) A comparison of wild-type yeast and zap1 mutants in synthetic complete medium with three different concentrations of zinc [13], in a long, unbroken, replicated chain of comparisons. Circles surrounded by a double line highlight the samples that turned out to be most important to their study.