FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces

28 Pags.- 8 Figs. 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.

Detalles Bibliográficos
Autores: Contreras-Moreira, Bruno, Sebastián Yagüe, Álvaro
Tipo de recurso: otro
Estado:Versión aceptada para publicación
Fecha de publicación:2016
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/136262
Acceso en línea:http://hdl.handle.net/10261/136262
Access Level:acceso abierto
Palabra clave:Bioinformatics
transcription factor
DNA binding
DNA motif
PSSM
protein domain
Promoter
cis-element
Database
open-access
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oai_identifier_str oai:digital.csic.es:10261/136262
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spelling FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfacesContreras-Moreira, BrunoSebastián Yagüe, ÁlvaroBioinformaticstranscription factorDNA bindingDNA motifPSSMprotein domainPromotercis-elementDatabaseopen-access28 Pags.- 8 Figs. 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.FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyzes.This work was funded by grant Euroinvestigación EUI2008-03612 under the framework of the Transnational (Germany, France, Spain) Cooperation within the PLANT-KBBE Initiative.Peer reviewedSpringer NatureEuropean CommissionPLANT-KBBEConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]201620162016info:eu-repo/semantics/otherhttp://purl.org/coar/resource_type/c_3248Postprintinfo:eu-repo/semantics/acceptedVersioninfo:eu-repo/semantics/bookParthttp://hdl.handle.net/10261/136262reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1007/978-1-4939-6396-6_17Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1362622026-05-22T06:33:51Z
dc.title.none.fl_str_mv FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
title FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
spellingShingle FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
Contreras-Moreira, Bruno
Bioinformatics
transcription factor
DNA binding
DNA motif
PSSM
protein domain
Promoter
cis-element
Database
open-access
title_short FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
title_full FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
title_fullStr FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
title_full_unstemmed FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
title_sort FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
dc.creator.none.fl_str_mv Contreras-Moreira, Bruno
Sebastián Yagüe, Álvaro
author Contreras-Moreira, Bruno
author_facet Contreras-Moreira, Bruno
Sebastián Yagüe, Álvaro
author_role author
author2 Sebastián Yagüe, Álvaro
author2_role author
dc.contributor.none.fl_str_mv European Commission
PLANT-KBBE
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Bioinformatics
transcription factor
DNA binding
DNA motif
PSSM
protein domain
Promoter
cis-element
Database
open-access
topic Bioinformatics
transcription factor
DNA binding
DNA motif
PSSM
protein domain
Promoter
cis-element
Database
open-access
description 28 Pags.- 8 Figs. 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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016
2016
dc.type.none.fl_str_mv info:eu-repo/semantics/other
http://purl.org/coar/resource_type/c_3248
Postprint
info:eu-repo/semantics/acceptedVersion
dc.type.openaire.fl_str_mv info:eu-repo/semantics/bookPart
format other
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/136262
url http://hdl.handle.net/10261/136262
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1007/978-1-4939-6396-6_17
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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