MotifMap: a human genome-wide map of candidate regulatory motif sites

Motivation: Achieving a comprehensive map of all the regulatory elements encoded in the human genome is a fundamental challenge of biomedical research. So far, only a small fraction of the regulatory elements have been characterized, and there is great interest in applying computational techniques to systematically discover these elements. Such efforts, however, have been significantly hindered by the overwhelming size of non-coding DNA regions and the statistical variability and complex spatial organizations of mammalian regulatory elements. Results: Here we combine information from multiple mammalian genomes to derive the first fairly comprehensive map of regulatory elements in the human genome. We develop a procedure for identifying regulatory sites, with high levels of conservation across different species, using a new scoring scheme, the Bayesian branch length score (BBLS). Using BBLS, we predict 1.5 million regulatory sites, corresponding to 380 known regulatory motifs, with an estimated false discovery rate (FDR) of