title: Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.
abstract: We generalize the computation of the Regulatory Potential (RP) score from two-way alignments of human and mouse to three-way alignments of human, mouse, and rat. This requires overcoming technical challenges that arise because the complexity of the models underlying the score increases exponentially with the number of species. Despite the close evolutionary proximity of rat to mouse, we find that adding the rat sequence increases our ability to predict genomic sites that regulate gene transcription. A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Kolbe
authors.forename: James
authors.initials: J
authors.lastname: Taylor
authors.forename: Laura
authors.initials: L
authors.lastname: Elnitski
authors.forename: Pallavi
authors.initials: P
authors.lastname: Eswara
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Ross
authors.initials: R
authors.lastname: Hardison
authors.forename: Francesca
authors.initials: F
authors.lastname: Chiaromonte
mesh_terms: D000199:Actins / Q000235:genetics; D000818:Animals; D022763:CCAAT-Enhancer-Binding Protein-alpha / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D004247:DNA / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D006801:Humans; D051379:Mice; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data
chemical_list: D000199:Actins; D022763:CCAAT-Enhancer-Binding Protein-alpha; D004247:DNA