Figure 4.

Venn diagram and clustering of genes with a significant transcriptional response to pH. The Venn diagram (a) is based on three pairwise comparisons. Each area in the Venn diagram is divided into subsets by the direction of the response in the different comparisons. The formation of dots in the squares shows the general tendency of the response, with the example of (b) having expression indices increasing with pH. Two dots on the same line means that no statistically significant difference was found between the two conditions. Each subset has been divided into clusters, as shown for the example subset (b). Predicted recognition motifs for cis-acting elements are shown (c). Sequence logos are made as described by Schneider and Stephens [63].