title: Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
abstract: The transcription factor affinity prediction (TRAP) method calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This protocol covers two other applications: (i) determining which transcription factors have the highest affinity in a set of sequences (illustrated with chromatin immunoprecipitation-sequencing (ChIP-seq) peaks), and (ii) finding which factor is the most affected by a regulatory single-nucleotide polymorphism. The protocol describes how to use the TRAP web tools to address these questions, and it also presents a way to run TRAP on random control sequences to better estimate the significance of the results. All of the tools are fully available online and do not need any additional installation. The complete protocol takes about 45 min, but each individual tool runs in a few minutes.
authors: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. thomas-c@molgen.mpg.de
authors: Morgane
authors: M
authors: Thomas-Chollier
authors: Andrew
authors: A
authors: Hufton
authors: Matthias
authors: M
authors: Heinig
authors: Sean
authors: S
authors: O'Keeffe
authors: Nassim El
authors: NE
authors: Masri
authors: Helge G
authors: HG
authors: Roider
authors: Thomas
authors: T
authors: Manke
authors: Martin
authors: M
authors: Vingron
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors