Motif predictions based on conservation-free and conserved promoters.

All promoters used in these predictions were inferred by ARACNe algorithm. We compared motif enrichment accuracy across the original promoters and conserved regions identified using alignment-based conservation with varying DNA-coverage proportions, and a combination of alignment-based and pattern-discovery based conservation. For alignment-based conservation, best performance was achieved at 10% DNA coverage, and this was used in conjunction with pattern-discovery based conservation at 10% DNA coverage to produce combined-conservation. A test is considered as successful if the most enriched motif identified using either the conservation-free or the combined-conservation promoters matched the known motif for the TF. We called it conservation-free and combined-conservation merged. The recall rate at this level was significantly better than that using conservation-free alone.