Association between the status of TFs and targets. (a) Contingency tables of the presence or absence of TFs and their targets in S. flexneri 2457T for both positive and negative regulatory interactions. The significance of the associations was calculated using the χ2 test. The association is stronger for negative regulatory interactions than it is for positive regulatory interactions. In a far larger fraction of positive than negative regulatory interactions, the TF is absent while the targets remain in the genome. (b) The strength of association between the presence or absence of TFs and that of their targets, as determined by the phi-coefficient. The association is stronger in bacteria closer to E. coli K12 than in more remote bacteria for both positive and negative regulatory interactions. In closely related bacteria, negative regulatory interactions (phi-coefficients represented by red bars) show stronger association than positive regulatory interactions (phi-coefficients represented by green bars). The values contained in the 60 contingency tables for all organisms in our study and their corresponding p values and phi-coefficients are listed in supplementary Table 2 in Additional data file 1.