PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1093/database/bay078 http://hdl.handle.net/11449/164649 |
Resumo: | Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE :(http//planc-te.cp.utfpr.edu.br), a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data. We identified a total of 14 350 overlaps between ncRNAs and TEs in 40 plant genomes. The database allows users to browse, search and download all ncRNA and TE data analysed. Overall, PlaNC-TE not only organizes data and provides insights about the relationship between ncRNA and TEs in plants but also helps improve genome annotation strategies. Moreover, this is the first database to provide resources to broadly investigate functions and mechanisms involving TEs and ncRNAs in plants. |
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Repositório Institucional da UNESP |
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PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plantsTransposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE :(http//planc-te.cp.utfpr.edu.br), a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data. We identified a total of 14 350 overlaps between ncRNAs and TEs in 40 plant genomes. The database allows users to browse, search and download all ncRNA and TE data analysed. Overall, PlaNC-TE not only organizes data and provides insights about the relationship between ncRNA and TEs in plants but also helps improve genome annotation strategies. Moreover, this is the first database to provide resources to broadly investigate functions and mechanisms involving TEs and ncRNAs in plants.Universidade Tecnologica Federal do ParanaCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Pro-Reitoria de Pesquisa e Pos-Graduacao (PROPPG-UTFPR)Univ Tecnol Fed Parana, Bioinformat Grad Program PPGBIOINFO, Dept Comp Sci, 1640 Ave Alberto Carazzai, BR-86300000 Cornelio Procopio, PR, BrazilUniv Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, 3900 Bandeirantes Ave, BR-14049900 Monte Alegre do Sul, SP, BrazilUNESP, Sao Paulo State Univ, Inst Biosci, Dept Bot, Av 24-A 1515, BR-13506900 Rio Claro, SP, BrazilUNESP, Sao Paulo State Univ, Inst Biosci, Dept Bot, Av 24-A 1515, BR-13506900 Rio Claro, SP, BrazilFAPESP: 2017/03052-2CNPq: 309642/2015-9Oxford Univ PressUniv Tecnol Fed ParanaUniversidade de São Paulo (USP)Universidade Estadual Paulista (Unesp)Fernandes Pedro, Daniel LonghiRodrigues Lorenzetti, Alan PericlesDomingues, Douglas Silva [UNESP]Paschoal, Alexandre Rossi2018-11-26T17:55:27Z2018-11-26T17:55:27Z2018-09-13info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article7application/pdfhttp://dx.doi.org/10.1093/database/bay078Database-the Journal Of Biological Databases And Curation. Oxford: Oxford Univ Press, 7 p., 2018.1758-0463http://hdl.handle.net/11449/16464910.1093/database/bay078WOS:000444756600001WOS000444756600001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengDatabase-the Journal Of Biological Databases And Curation1,791info:eu-repo/semantics/openAccess2023-12-27T06:23:09Zoai:repositorio.unesp.br:11449/164649Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:27:47.102973Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
title |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
spellingShingle |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants Fernandes Pedro, Daniel Longhi |
title_short |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
title_full |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
title_fullStr |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
title_full_unstemmed |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
title_sort |
PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants |
author |
Fernandes Pedro, Daniel Longhi |
author_facet |
Fernandes Pedro, Daniel Longhi Rodrigues Lorenzetti, Alan Pericles Domingues, Douglas Silva [UNESP] Paschoal, Alexandre Rossi |
author_role |
author |
author2 |
Rodrigues Lorenzetti, Alan Pericles Domingues, Douglas Silva [UNESP] Paschoal, Alexandre Rossi |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Univ Tecnol Fed Parana Universidade de São Paulo (USP) Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Fernandes Pedro, Daniel Longhi Rodrigues Lorenzetti, Alan Pericles Domingues, Douglas Silva [UNESP] Paschoal, Alexandre Rossi |
description |
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE :(http//planc-te.cp.utfpr.edu.br), a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data. We identified a total of 14 350 overlaps between ncRNAs and TEs in 40 plant genomes. The database allows users to browse, search and download all ncRNA and TE data analysed. Overall, PlaNC-TE not only organizes data and provides insights about the relationship between ncRNA and TEs in plants but also helps improve genome annotation strategies. Moreover, this is the first database to provide resources to broadly investigate functions and mechanisms involving TEs and ncRNAs in plants. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:55:27Z 2018-11-26T17:55:27Z 2018-09-13 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1093/database/bay078 Database-the Journal Of Biological Databases And Curation. Oxford: Oxford Univ Press, 7 p., 2018. 1758-0463 http://hdl.handle.net/11449/164649 10.1093/database/bay078 WOS:000444756600001 WOS000444756600001.pdf |
url |
http://dx.doi.org/10.1093/database/bay078 http://hdl.handle.net/11449/164649 |
identifier_str_mv |
Database-the Journal Of Biological Databases And Curation. Oxford: Oxford Univ Press, 7 p., 2018. 1758-0463 10.1093/database/bay078 WOS:000444756600001 WOS000444756600001.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Database-the Journal Of Biological Databases And Curation 1,791 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
7 application/pdf |
dc.publisher.none.fl_str_mv |
Oxford Univ Press |
publisher.none.fl_str_mv |
Oxford Univ Press |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129322819518464 |