Additional file 8.

Figure S3. Detailed heat map for each gene cluster from main text Figure 5 (H2O2 exposure). Data for those genes dependent on VNG0258H for appropriate expression are shown (i.e. main text Figures 5A-G). Gene names are listed on the right of each heat map. Detailed annotations and COG category memberships (main text Figure 7A) for each these genes are listed in Additional file 4: Table S2. In each heat map, red represents induction, whereas blue represents repression. VNG0258H-independent genes (Cluster 4, Figure 5H and J) are not included in the Figure for brevity and clarity, but expression data and annotations for these genes are included in Additional file 4: Table S2. (A) Cluster 1 includes genes that were differentially expressed in the ΔVNG0258H mutant vs Δura3 parent strain regardless of growth condition (main text Figures 5A-B). Cluster 1a (main text Figure 5A) depicts those 33 genes that are over-expressed in the ΔVNG0258H mutant (i.e. RosR is required to repress these genes). Cluster 1b (main text Figure 5B) depicts those 30 genes that are under-expressed in the ΔVNG0258H mutant (i.e. VNG0258H is required to activate these genes). (B) Cluster 2 includes genes that were differentially expressed in the ΔVNG0258H mutant vs Δura3 parent strain in the presence of H2O2 (main text Figures 5C-D). Cluster 2a (main text Figure 5C) contains those 43 genes that are over-expressed in the ΔVNG0258H mutant in response to H2O2 (i.e. VNG0258H is required to repress these genes in response to H2O2). Cluster 2b (main text Figure 5D) contains those genes that are under-expressed in the ΔVNG0258H mutant in response to H2O2 (i.e. VNG0258H is required to induce them). (C) Cluster 3 includes genes that were differentially expressed in the ΔVNG0258H mutant vs Δura3 parent strain in the absence of H2O2 (main text Figure 5E). (D) Growth of Δura3 parent and ΔVNG0258H cultures for gene expression microarray analysis. Black curves represent growth data for the two biological replicate cultures of Δura3, whereas red curves are data for the two biological replicate cultures of ΔVNG0258H. Dotted arrows on the curves indicate the start and end of sampling over the time courses shown in the heat maps, whereas the solid arrow shows the time of H2O2 addition to the cultures.

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Sharma et al. BMC Genomics 2012 13:351   doi:10.1186/1471-2164-13-351