Figure 6

Incorporation of conservation and word pairs provided more informative average expression profiles. Groups of genes whose TCRs contained various sequence features were summarized by the average of their gene-expression profiles. Each row in these diagrams represents a given gene group's average expression pattern under the conditions shown in each column: exposure to increasing concentrations of cadmium chloride (from 0.05 mM to 0.4 mM); 20 min after heat shock to 37°C (from 17°C, 21°C, 25°C, 29°C, and 33°C); an amino-acid starvation time course; a nitrogen-source depletion time course; progression into stationary phase (2 h, 4 h, 6 h, 8 h, 10 h, 12 h, 1 day, 2 days, 3 days, 5 days of growth) [30]. Representative conserved word-pair templates were chosen for analysis, corresponding to: (a) Msn2/4p-like sequences (CTCCCC and CCCTTA); (b) Cbf1p (CACGTG) and Met31/32p (TGTGGC) binding sites; (c) Mig1p (ACCCCA) and Ume6 (CCGCCG) binding sites; (d) Msn2/4p-like (CCCCTT) and Hsf1p-like (GAGAAA) sequences. For each of the panels (a-d) each row represents the average expression profile for gene groups chosen by different sequence features in their TCRs: single words found in S. cerevisiae (rows 1 and 2); single words conserved in three or more Saccharomyces genomes (rows 3 and 4); word pairs found in S. cerevisiae (row 5); word pairs conserved in three or more Saccharomyces genomes (row 6). Arrows above the columns indicate conditions under which gene groups sharing the conserved word-pair template (row 6) were significantly associated with gene-expression changes, at a p-value of 0.001 (K-S test after FDR correction for multiple testing).