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

被引：180
|
作者：
Thomas-Chollier, Morgane [1 ]
Hufton, Andrew [1 ]
Heinig, Matthias [1 ]
O'Keeffe, Sean [1 ]
El Masri, Nassim [1 ]
Roider, Helge G. [1 ]
Manke, Thomas [2 ]
Vingron, Martin [1 ]
机构：
[1] Max Planck Inst Mol Genet, Dept Computat Mol Biol, D-14195 Berlin, Germany
[2] Max Planck Inst Immunobiol & Epigenet, Freiburg, Germany
来源：
NATURE PROTOCOLS | 2011年 / 6卷 / 12期
关键词：
DNA; IDENTIFICATION; ASSOCIATION; WORKBENCH; RSAT;
D O I：
10.1038/nprot.2011.409
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
引用
收藏
页码：1860 / 1869
页数：10
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