title: Annotating significant pairs of transcription factor binding sites in regulatory DNA.
abstract: In the presented work we search for transcription factor binding sites (BS) by including additional information about typical BS patterns. The new proposed score combines the ordinary profile score based on TRANSFAC-matrices together with a score based on pairs of BS. The latter score positively weights pairs of BS that tend to occur together in many regulatory DNA-sequences, in contrast to a random background model. The empirical BS pair frequencies result from our evaluation of a large dataset of orthologous genes.
authors.affiliation: Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin, Germany. Katja.Rateitschak@molgen.mpg.de
authors.forename: Katja
authors.initials: K
authors.lastname: Rateitschak
authors.forename: Tobias
authors.initials: T
authors.lastname: Müller
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D017124:Conserved Sequence; D004268:DNA-Binding Proteins / Q000378:metabolism*; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D006801:Humans; D051379:Mice; D024510:Muscle Development / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors