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  A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

Thomas-Chollier, M., Darbo, E., Herrmann, C., Defrance, M., Thieffry, D., & van Helden, J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nature Protocols, 7(8), 1551-1568. doi:10.1038/nprot.2012.088.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E86C-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E86D-D
Genre: Journal Article

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 Creators:
Thomas-Chollier, Morgane1, Author              
Darbo, Elodie2, Author
Herrmann, Carl2, Author
Defrance, Matthieu3, Author
Thieffry, Denis2, 4, Author
van Helden, Jacques2, 5, Author
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Ggermany, ou_1433547              
2Technological Advances for Genomics and Clinics, Institut National de la Santé et de la Recherche Médicale (INSERM) U928 and Université de la Méditerranée, Marseille, France, ou_persistent22              
3Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico, ou_persistent22              
4Institut de Biologie de l'Ecole Normale Supérieure—Centre National de la Recherche Scientifique Unité Mixte de Recherche (CNRS UMR) 8197 and INSERM U1024, Paris, France, ou_persistent22              
5Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium, ou_persistent22              

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Free keywords: Algorithms Animals Binding Sites Chromatin Immunoprecipitation/*methods Drosophila Proteins/genetics Drosophila melanogaster/embryology/genetics Embryo, Nonmammalian Genomics/*methods Kruppel-Like Transcription Factors/genetics Mice *Nucleotide Motifs Sequence Analysis, DNA/*methods *Software Time Factors Transcription Factors/genetics/metabolism *Workflow
 Abstract: This protocol explains how to use the online integrated pipeline 'peak-motifs' (http://rsat.ulb.ac.be/rsat/) to predict motifs and binding sites in full-size peak sets obtained by chromatin immunoprecipitation-sequencing (ChIP-seq) or related technologies. The workflow combines four time- and memory-efficient motif discovery algorithms to extract significant motifs from the sequences. Discovered motifs are compared with databases of known motifs to identify potentially bound transcription factors. Sequences are scanned to predict transcription factor binding sites and analyze their enrichment and positional distribution relative to peak centers. Peaks and binding sites are exported as BED tracks that can be uploaded into the University of California Santa Cruz (UCSC) genome browser for visualization in the genomic context. This protocol is illustrated with the analysis of a set of 6,000 peaks (8 Mb in total) bound by the Drosophila transcription factor Kruppel. The complete workflow is achieved in about 25 min of computational time on the Regulatory Sequence Analysis Tools (RSAT) Web server. This protocol can be followed in about 1 h.

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Language(s): eng - English
 Dates: 2012-07-26
 Publication Status: Published online
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 Rev. Method: Peer
 Identifiers: DOI: 10.1038/nprot.2012.088
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Title: Nature Protocols
  Other : Nat. Protoc.
Source Genre: Journal
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Pages: - Volume / Issue: 7 (8) Sequence Number: - Start / End Page: 1551 - 1568 Identifier: ISSN: 1750-2799
CoNE: /journals/resource/1000000000223800_1