Fig. 3
Transcription factor/Sigma factor − target gene regulatory network response to sudden carbon excess. Transcription factor (TF)/Sigma factor/(SF) − target gene network map only considering expressed genes responsive to the addition of the single glucose pulse (absolute log2 fold change ≥ 1.5) and TF/SF combinations which have at least significant activating or inhibiting interactions (corresponding corrected p-value < 0.0025) with at least 9 genes within one cluster (for details refer to Materials and methods and Additional file 2). Line endings with arrow indicate activation and line endings with bar represent inhibition of genes through respective TF/SF combinations. For example, a line ending with an arrow pointing to a cluster showing down-regulated genes indicates that the respective TF/SF combination loses control. The intensity of the blue color indicates the significance of interaction (log10 nominal p-value, dark blue highly significant, see insert for color code meaning). The width of the blue line (and number close to it) connecting TF/SF combination and cluster (clusters as in Fig. 2) indicate the number of genes in the respective cluster controlled by this TF/SF combination. The gray dotted lines connecting TF or SF and cluster indicate the assignment of the TF or SF to a cluster according to its own expression profile. For simplicity, short abbreviations of TFs represent the active form (e.g., CRP represents CRP-cAMP) and a gray background indicates that the active form of the TF is generated by posttranslational modification. The color codes of the frames around the cluster indicate transcriptional down- (green), non-uniform (greenish and reddish) and up-regulation (red) of the genes in the corresponding cluster (see also 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 color codes of the frames around the TFs and SFs indicate expression level of respective TF and SF genes, respectively (color code as described above for cluster frames)