Figure 2.

Clustering of genes regulated during environmental stress. (a) Hierarchical cluster analysis with columns representing experimental time points and rows representing the 1,355 genes that were regulated after exposure to H2O2, at the level of either mRNA and/or translation as defined in Table 1. Columns 1 and 2: mRNA expression levels after 15 and 60 minutes in stress, respectively, relative to expression in the same cells before stress are color coded as indicated at the bottom. Columns 3 and 4: translation ratios (Figure 1c; Additional file 1; Materials and methods) after 15 and 60 minutes in stress, respectively, are color coded as indicated at the bottom. Data from biologically repeated samples are averaged, with missing data in gray. The red bars indicate clusters 1 and 2 described in the text. The graphs at right show average translation profiles for the genes of clusters 1 and 2 before and after exposure to H2O2. Blue lines, control (unstressed) samples; orange lines, 15 minutes after stress; red lines, 60 minutes after stress. Multiple lines of the same color represent average translation profiles from independent biological repeats. Annotated gene lists of these clusters are provided in Additional file 3. (b) Cluster analysis as in (a) for the 1,071 genes that were regulated after exposure to 39°C, at the level of either mRNA and/or translation (Table 1). The red bar indicates cluster 3 described in the text. The graph at right shows the average translation profiles for cluster 3 genes before as well as 15 and 60 minutes after exposure to 39°C, with details as in (a). An annotated gene list of cluster 3 is provided in Additional file 3. (c) Cluster analysis as in (a) for the 233 genes that were regulated after exposure to DNA damage, at the level of either mRNA and/or translation (Table 1).

Lackner et al. Genome Biology 2012 13:R25   doi:10.1186/gb-2012-13-4-r25
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