Figure 9. IF-THEN rules encompassing submotifs and distances between PhoP BSs and RNAP BSs.

A) Cells correspond to IF-THEN rules. The antecedent of the rules is composed of submotifs (vertical left panel) and the distances between PhoP BSs and RNAP BSs (horizontal panel). The submotifs are encoded as fuzzy sets based on their score distributions. The distances are approximated by their distributions (close, medium, and far distances from left to right panels), and also encoded by fuzzy sets. Both antecedents are combined a fuzzy AND operator (i.e., product). The consequent of a rule classifies PhoP BSs in the unit interval as a function of the antecedents (1: high, 0: low). Rules are activated concurrently, when they exceed each rule-specific threshold. The isobars show the degree of membership of the training set to the rules (white: none; red: high; blue: low). B) Synthesis of the PhoP BSs recognized by the most representative IF-THEN rules that distinguish E. coli K-12 (green) from S. typhimurium (red) genomes. The percentage of BSs recognized by each rule in each genome is represented by the height of the bars. Submotifs were compressed into their most general families (i.e., S01, S05, and S08 & S09) for simplicity. Three subsets of rules (i.e., S01 and close, S08 & S09 and close; and S08 & S09 and medium) are similarly distributed in both genomes (grey boxes). Specific rules in E. coli (i.e., S05 and close, green boxes), and in Salmonella (S01 and medium; S05 and far; and S8 & S9 and far, red boxes) were also identified. C) Same as in B) but applying IF-THEN rules in Y. pestis. No rules were identified for the S05 family of submotifs, as well as for far distances.