Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

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...

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Published inNature protocols Vol. 6; no. 12; pp. 1860 - 1869
Main Authors Thomas-Chollier, Morgane, Hufton, Andrew, Heinig, Matthias, O'Keeffe, Sean, Masri, Nassim El, Roider, Helge G, Manke, Thomas, Vingron, Martin
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.12.2011
Nature Publishing Group
Subjects
631/114
631/1647/2204
631/45/612/822
Analytical Chemistry
Binding Sites
Biological Techniques
Biomedical and Life Sciences
Chromatin Immunoprecipitation - methods
Computational Biology/Bioinformatics
Deoxyribonucleic acid
DNA
Life Sciences
Methods
Microarrays
Organic Chemistry
Physiological aspects
Polymorphism, Single Nucleotide
Promoter Regions, Genetic
Protein binding
Protocol
Quantitative Methods
Single nucleotide polymorphisms
Software
Transcription factors
Transcription Factors - metabolism
Germany
Online AccessGet full text
ISSN1754-2189
1750-2799
1750-2799
DOI10.1038/nprot.2011.409

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Summary: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.
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ISSN:1754-2189
1750-2799
1750-2799
DOI:10.1038/nprot.2011.409