Figure 7. The influence of operator position and secondary transcription factors on the ability to predict BqsR-mediated gene regulation.

(A) For the genes predicted in Fig. 6, the error in prediction, defined as the ratio of predicted over experimentally measured expression levels, is shown as a function of operator positions relative to the transcription start site. A prediction error of 1 indicates the measurement exactly matched the prediction. (B) Error in prediction plotted as a function of the number of BqsR binding sites found in the promoter region. (C) Venn diagrams showing regulon overlaps between the predicted genes and selected transcriptional regulators with statistically significant overlap. See section “Comparison to other operons” in Supplemental Materials. (D) Position weight matrices for 12 transcription factors were used to identify which of the predicted genes were likely to be coregulated by an additional transcription factor. The upper graph shows the number of promoter regions containing a potential binding site for a second transcription factor. Bars on the bottom graph show the average prediction error for each set of genes containing a secondary transcription factor; the larger the ratio, the greater the error.