Figure 2.

Global comparison of the S. cerevisiae and C. glabrata chemical stress responses based on DCA and MatrixREDUCE analyses. (a) We analyzed 718 orthologous gene pairs for which at least one gene displayed a change in expression in response to benomyl stress using the DCA method [10]. The DCA cluster pairs of orthologous genes according to their expression in each species (see Additional data file 3 for a complete description of the DCA method). S. cerevisiae was used as the 'reference' yeast whereas C. glabrata was used as the 'target' yeast. Eight clusters were obtained after primary hierarchical clustering using the S. cerevisiae expression profiles. Each cluster was then split into two subclusters (labeled 'a' and 'b') after secondary hierarchical clustering using the C. glabrata expression profiles. Gene expression profiles are indicated with a color code [80]: green for down-regulated genes and red for up-regulated genes. Based on the mean correlations between gene expression levels within and between 'a' and 'b' subgroups, eight conservation clusters were defined: three clusters displaying 'full conservation' (clusters 2, 7 and 8); three clusters displaying 'partial conservation' (clusters 1, 3 and 6); and two clusters displaying 'split conservation' (clusters 4 and 5). The biological relevance of these clusters is discussed in Additional data file 4. (b) Three pairs of PSAMs identified with the MatrixREDUCE algorithm [31] and that exhibited significant Pearson correlations (r > 0.6) are shown in the panel on the left. They correspond to specific regulatory sequences that are evolutionarily conserved between S. cerevisiae and C. glabrata. The panel on the right shows the frequency of occurrence of PSAM in 50 bp windows of the gene clusters identified with the DCA. Background genomic frequency is indicated in black (dashed line); the frequency in conserved parts of DCA clusters is indicated in red (clusters 1b, 2 and 3b for down-regulated genes, and clusters 6b, 7 and 8 for up-regulated clusters); and the frequency in non-conserved parts of DCA clusters is indicated in yellow (clusters 1a, 3a and 4 for down-regulated genes, and clusters 5 and 6a for up-regulated clusters). Together, the DCA and MatrixREDUCE results allowed the identification of a set of orthologous genes whose expression and regulation is conserved between the two species examined here.