title: RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.
abstract: The plant-dedicated mirror of the Regulatory Sequence Analysis Tools (RSAT, http://plants.rsat.eu ) offers specialized options for researchers dealing with plant transcriptional regulation. The website contains whole-sequenced genomes from species regularly updated from Ensembl Plants and other sources (currently 40), and supports an array of tasks frequently required for the analysis of regulatory sequences, such as retrieving upstream sequences, motif discovery, motif comparison, and pattern matching. RSAT::Plants also integrates the footprintDB collection of DNA motifs. This protocol explains step-by-step how to discover DNA motifs in regulatory regions of clusters of co-expressed genes in plants. It also explains how to empirically control the significance of the result, and how to associate the discovered motifs with putative binding factors.
authors.affiliation: Estación Experimental de Aula Dei-CSIC, Av. Montañana 1.005, 50059, Zaragoza, Spain. bcontreras@eead.csic.es.|Fundación ARAID, calle María de Luna 11, 50018, Zaragoza, Spain. bcontreras@eead.csic.es.
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
authors.affiliation: INSERM, U1090 TAGC, Aix Marseille University, U1090 TAGC, Marseille, 13288, France.
authors.forename: Jaime A
authors.initials: JA
authors.lastname: Castro-Mondragon
authors.affiliation: INSERM, U1090 TAGC, Aix Marseille University, U1090 TAGC, 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.
authors.forename: Carlos P
authors.initials: CP
authors.lastname: Cantalapiedra
authors.affiliation: INSERM, U1090 TAGC, Aix Marseille University, U1090 TAGC, Marseille, 13288, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: van Helden
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059372:Nucleotide Motifs / Q000235:genetics; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors
keywords: Cluster; Co-expression; DNA motif; Position-weight matrix; Upstream sequence