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.
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Acknowledgements
This work was supported by the Alexander von Humboldt foundation. We thank A. Mysickova for her insightful comments on this protocol, and S. Haas for helpful discussions.
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H.G.R., T.M. and M.V. developed the original TRAP approach and the P value calculation. M.H., T.M. and M.V. developed the sTRAP approach. A.H. implemented the combination of P values approach and the first version of the web tools. M.T.-C. integrated the different approaches, added new matrix and background models, and supervised the remodeling of the website by N.E.M. S.O. helped in the implementation of the website. M.T.-C. wrote the manuscript, and A.H., S.O., H.G.R. and T.M. edited the manuscript.
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Thomas-Chollier, M., Hufton, A., Heinig, M. et al. Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat Protoc 6, 1860–1869 (2011). https://doi.org/10.1038/nprot.2011.409
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DOI: https://doi.org/10.1038/nprot.2011.409
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