FIGURE 2. Characterization of the regulatory network related to the aerobic–anaerobic shift.

a, The locus numbers, gene names and the log2 ratio (L2R) of gene expression (aerobic to anaerobic) are shown for all model genes with either predicted or observed changes in expression (genes were divided into the same functional groups as in Fig. 1). The L2R values are shaded depending on the magnitude of the expression shift, and those enclosed by a box indicate a statistically significant change in expression (P < 0.007, FDR < 5%). Comparisons between the experimental data and model predictions are also shown, where v1 (iMC1010^v1) and v2 (iMC1010^v2) designate the model used in the predictions. Filled and open symbols indicate model predictions and experimental data, respectively; rectangles indicate no change in gene expression; triangles indicate a change in expression, as well as the direction of change (upregulated or downregulated). b, Comparison of the predicted and observed expression changes for the v1 and v2 models. A question mark indicates either that the given gene was not included in the model or that no expression data were obtained for a given shift; other symbols are the same as in a. c, Systematic perturbation analysis was used to determine the transcription factors responsible for the expression change. The transcription factors knocked out in the six strains are shown on top. Each row indicates a pattern of knockout strains in which differential expression was abolished. The number of genes that show this pattern is indicated on the right. Thus, the first row indicates that for 73 of the 437 genes that showed differential expression in the wild-type strain (or 20 of the 151 genes accounted for by the model), the observed differential expression was abolished only in the arcAfnr knockout strain.