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RSAT::Plants: Motif discovery in ChIP-Seq peaks of plant genomes

AuthorsCastro-Mondragón, Jaime A.; Rioualen, Claire; Contreras-Moreira, Bruno CSIC ORCID ; van Helden, Jacques
KeywordsChromatin immunoprecipitation DNA-sequencing (ChIP-seq)
Transcription factor (TF)
Transcription factor binding motifs (TFBM)
Transcription factor binding site (TFBS)
Gene ontology (GO)
Functional enrichment
Issue DateAug-2016
CitationCastro-Mondragon J, Rioualen C, Contreras-Moreira B, van Helden J. RSAT::Plants: Motif discovery in ChIP-Seq peaks of plant genomes. In: Hehl R (ed.), Plant Synthetic Promoters (Methods in Molecular Biology 1482: 297-322), New York, Springer Science+Business Media. DOI: 10.1007/978-1-4939-6396-6_19 (2016)
SeriesMethods in Molecular Biology
AbstractIn this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana.
Description26 Pags.- 8 Figs.- 2 Tabls. The definitive version is available at: http://link.springer.com/bookseries/7651 and http://link.springer.com/book/10.1007/978-1-4939-6396-6
Publisher version (URL)http://dx.doi.org/10.1007/978-1-4939-6396-6_19
ISBN978-1-4939-6394-2 (Print)
978-1-4939-6396-6 (Online)
Appears in Collections:(EEAD) Libros y partes de libros
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