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

AutorCastro-Mondragon, Jaime; Rioualen, Claire; Contreras-Moreira, Bruno ; van Helden, Jacques
Palabras claveChromatin immunoprecipitation DNA-sequencing (ChIP-seq)
Transcription factor (TF)
Transcription factor binding motifs (TFBM)
Transcription factor binding site (TFBS)
Gene ontology (GO)
Functional enrichment
Fecha de publicaciónago-2016
EditorSpringer
CitaciónCastro-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)
SerieMethods in Molecular Biology
1482
ResumenIn 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.
Descripción26 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
Versión del editorhttp://dx.doi.org/10.1007/978-1-4939-6396-6_19
URIhttp://hdl.handle.net/10261/136254
DOI10.1007/978-1-4939-6396-6_19
ISBN978-1-4939-6394-2 (Print)
978-1-4939-6396-6 (Online)
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