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dc.contributor.authorCastro-Mondragón, Jaime A.es_ES
dc.contributor.authorRioualen, Clairees_ES
dc.contributor.authorContreras-Moreira, Brunoes_ES
dc.contributor.authorvan Helden, Jacqueses_ES
dc.date.accessioned2016-09-02T08:14:58Z-
dc.date.available2016-09-02T08:14:58Z-
dc.date.issued2016-08-
dc.identifier.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)es_ES
dc.identifier.isbn978-1-4939-6394-2 (Print)-
dc.identifier.isbn978-1-4939-6396-6 (Online)-
dc.identifier.urihttp://hdl.handle.net/10261/136254-
dc.description26 Pags.- 8 Figs.- 2 Tabls. The definitive version is available at: http://link.springer.com/bookseries/7651 and http://link.springer.com/book/10.1007/978-1-4939-6396-6es_ES
dc.description.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.es_ES
dc.description.sponsorshipThis work was funded in part by Fundación ARAID and by the EnseignantsChercheurs invités program of Aix-Marseille Université (to B.C.M.). C.R. was supported by the France Génomique National infrastructure, funded as part of the Investissements d’Avenir, program managed by the Agence Nationale pour la Recherche (contract ANR-10-INBS-09). J.C-M PhD grant is funded by the Ecole Doctorale des Sciences de la Vie et de la Santé (EDSVS), AixMarseille Université.es_ES
dc.language.isoenges_ES
dc.publisherSpringer Naturees_ES
dc.relation.ispartofseriesMethods in Molecular Biologyes_ES
dc.relation.ispartofseries1482es_ES
dc.rightsopenAccessen_EN
dc.subjectChromatin immunoprecipitation DNA-sequencing (ChIP-seq)es_ES
dc.subjectTranscription factor (TF)es_ES
dc.subjectTranscription factor binding motifs (TFBM)es_ES
dc.subjectTranscription factor binding site (TFBS)es_ES
dc.subjectGene ontologyes_ES
dc.subjectFunctional enrichmentes_ES
dc.titleRSAT::Plants: Motif discovery in ChIP-Seq peaks of plant genomeses_ES
dc.typecapítulo de libroes_ES
dc.identifier.doi10.1007/978-1-4939-6396-6_19-
dc.description.peerreviewedPeer reviewedes_ES
dc.relation.publisherversionhttp://dx.doi.org/10.1007/978-1-4939-6396-6_19es_ES
dc.embargo.terms2017-08-31es_ES
dc.contributor.funderARAID Foundationes_ES
dc.contributor.funderAix-Marseille Universitées_ES
dc.contributor.funderAgence Nationale de la Recherche (France)es_ES
dc.relation.csices_ES
oprm.item.hasRevisionno ko 0 false*
dc.identifier.funderhttp://dx.doi.org/10.13039/100007586es_ES
dc.identifier.funderhttp://dx.doi.org/10.13039/501100001665es_ES
dc.type.coarhttp://purl.org/coar/resource_type/c_3248es_ES
item.openairetypecapítulo de libro-
item.cerifentitytypePublications-
item.languageiso639-1en-
item.grantfulltextopen-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.fulltextWith Fulltext-
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