Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison

Abstract

As the number of sequenced genomes has grown, the questions of which species are most useful and how many genomes are sufficient for comparison have become increasingly important for comparative genomics studies. We have systematically addressed these questions with respect to phylogenetic footprinting of transcription factor (TF) binding sites in the γ-proteobacteria, and have evaluated the statistical significance of our motif predictions. We used a study set of 166Escherichia coli genes that have experimentally identified TF binding sites upstream of the gene, with orthologous data from nine additional γ-proteobacteria for phylogenetic footprinting. Just three species were sufficient for ∼74.0% of the motif predictions to correspond to the experimentally reported E. coli sites, and important characteristics to consider when choosing species were phylogenetic distance, genome size, and natural habitat. We also performed simulations using randomized data to determine the critical maximum a posteriori probability (MAP) values for statistical significance of our motif predictions (P = 0.05). Approximately 60% of motif predictions containing sites from just three species had average MAP values above these critical MAP values. The inclusion of a species very closely related to E. coliincreased the number of statistically significant motif predictions, despite substantially increasing the critical MAP value.[Supplemental material is available online athttp://www.genome.org. In addition, our motif predictions for the study set and the entire E. coli genome are available online athttp://www.wadsworth.org/resnres/bioinfo/.]