We extended the number of genomes used in the phylogenic similarity analysis from 134 to 229 and used the E. coli TRN as the training set in contrast to the gene-gene pair training set suggested by [20]. Fig. 8 shows the probability distributions for the training (gene/TF interactions in the preliminary TRN) and complete (all possible gene/TF interactions) sets. Phylogenic similarity outperforms the GO and FTF methodologies. As in the case for GO similarity, the results are better than those obtained earlier (Fig. 4 of [20]) due to the gene-TF versus the gene-gene based approach.