Fig. 2
Transcriptome response to sudden carbon excess: determination of affected biological processes. Transcript data of differentially expressed genes with a similar change in the time-course pattern after the addition of the single glucose pulse were partitioned into clusters based on the background information of transcription factor (TF)/sigma factor (SF) − target gene interaction from RegulonDB database (http://regulondb.ccg.unam.mx/) [21, 22]. The constrained k-means clustering charts (Clusters 1–14) show the mean scaled time-dependent gene expression profiles (log2 fold change) with standard deviation averaged over the genes belonging to the respective cluster. The number of genes within a specific cluster is indicated on top of the cluster graph. The abscissa shows the time after the glucose pulse in hours and the ordinate the normalized log2 ratio of the differentially expressed genes (with the highest or lowest log2 ratio in the corresponding cluster). Clusters were grouped as follows: down-regulated (Clusters 1–4), non-uniform (Clusters 5–11), and up-regulated genes (Clusters 11–14). Frame color codes indicate down- (green), non-uniform (greenish and reddish) and up-regulation (red) of the genes in the corresponding cluster (see insert for color code meaning, inner and outer frames correspond to non-uniform regulation in the initial or later phases after the glucose pulse, respectively). The semantic map of over-represented GO categories of the ontology “biological process” in the obtained clusters was calculated using the web service “REVIGO” [23] applying the following criteria; number of differentially-expressed genes in the corresponding GO category (represented as disc) belonging to one cluster is larger than 9 and the corrected p-value lower than 0.0025 (for details refer to Materials and methods and Additional file 2). The disc color in the semantic map indicates the significance of over-representation of the category (log10 nominal p-value, dark blue highly significant, see insert for color code meaning) and the disc size the proportionality to the log number of genes in the category. Clusters containing genes of over-represented GO categories are connected by arrows with the respective GO category discs