title: RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.
abstract: In 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.
authors.affiliation: INSERM, U1090 TAGC, Aix Marseille University, Marseille, 13288, France.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Castro-Mondragon
authors.affiliation: INSERM, U1090 TAGC, Aix Marseille University, Marseille, 13288, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Rioualen
authors.affiliation: Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, 50059, Zaragoza, Spain.|Fundación ARAID, calle María de Luna 11, 50018, Zaragoza, Spain.
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.affiliation: INSERM, U1090 TAGC, Aix Marseille University, Marseille, 13288, France. Jacques.van-Helden@univ-amu.fr.
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D059372:Nucleotide Motifs / Q000235:genetics; D050436:Regulatory Elements, Transcriptional; D012984:Software
keywords: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq); Functional enrichment; Gene ontology (GO); Transcription factor (TF); Transcription factor binding motifs (TFBM); Transcription factor binding site (TFBS)