Fig. 4

Regulon bubble plots. A Average fold changes (av-FC) are plotted against the mean absolute deviation of the fold change (MAD av-FC) for the 3 h (left) and 6 h (right) samples. B Average fold-changes plotted against the fraction of regulon genes corresponding to the most likely regulation for the 3 h (left) and 6 h (right) samples. Bubble size indicates the number of regulon genes. Colour intensities indicate average p-values of the genes in the regulon classified from dark to light according to average p-values of < 0.0625, < 0.125, < 0.25, < 0.5. For clarity, regulons with average p-values ≥ 0.5 are not shown. Of note, the average fold changes, MAD, p-values and bubble sizes are based on the regulon genes that correspond to the most likely activity state of the regulator. This state, being either activated or repressed, is based on the largest fraction of regulon genes that show a fold change corresponding to one of these two activity states. The CtsR regulon is indicated in red