Figure 5.

Statistical significance of PhoP-binding site orientation. (A) PhoP-binding sites were discovered in both possible orientations relative to the open reading frame, even though all published PhoP-binding sites are reportedly only in one (i.e. direct) orientation. To test the hypothesis that the genome harbors the PhoP-binding site in either orientation, we collected the number of PhoP-binding sites both in intergenic and coding regions of the Salmonella and E. coli genomes at different specificity levels. % indicates the relationship with the maximum score obtained by the Consensus/Patser program with a single consensus motif. Using a 95% confidence interval, we could not reject the null hypothesis using one-way ANOVA. (B) Multiple tests illustrates that we did not find significant differences in pairwise comparisons among six sets generated by splitting the data by regions, motif scores and genomes (we use Matlab multicompare routine with corrections for multiple tests). The horizontal axis corresponds to rows in (A), and the vertical axis illustrates the group means of the columns in (B).