mirtronDB: a mirtron knowledge base
Resumo
Os mirtrons surgem de introns curtos com clivagem atípica usando o mecanismo de splicing. Até hoje não existe um repositório que organiza e centraliza os dados públicos de mitrons. De modo a preencher essa lacuna, apresenta-se o mirtronDB, o primeiro banco de dados dedicado aos mirtrons (http://mirtrondb.cp.utfpr.edu.br). MirtronDB contém um total de 1.407 precursores e 2.426 sequências maduras de mirtron em 18 espécies. MirtronDB é um recurso especializado que disponibiliza a comunidade científica uma plataforma amigável sobre oconhecimento dos mirtron. Este trabalho é baseado na publicação original na Bioinformatics IF: 5,481 (https://doi.org/10.1093/bioinformatics/btz153).
Palavras-chave:
Modelagem e integração dados biológicos, Banco de dados, Mineração de dados, Análise de dados, Bioinformática.
Referências
Agarwal, V. et al. (2015) Predicting effective microRNA target sites in mammalian mRNAs, Elife, 4.
Bonnet, E. et al. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics, Bioinformatics, 26, 1566-1568.
Budak, H. and Akpinar, B. (2015) Plant miRNAs: biogenesis, organization and origins, Functional & Integrative Genomics, 15, 523-531.
Dai, X. et al. (2018) psRNATarget: a plant small RNA target analysis server (2017 release), Nucleic Acids Research.
Das, S. et al. (2018) miRwayDB: a database for experimentally validated microRNA- pathway associations in pathophysiological conditions. Database (Oxford). 2018: bay023.
Fonseca B., Domingues D., Paschoal AR. mirtronDB: a mirtron knowledge base. Bioinformatics. btz153. doi: 10.1093/bioinformatics/btz153.
Gallart, A. et al. (2015) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Research, 44, D1161-D1166.
Griffiths-Jones, S. et al. (2006) miRBase: microRNA sequences, targets and gene nomenclature, Nucleic Acids Research, 34, D140-D144.
Grzegorz, R. et al. (2018) Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods, Scientific Reports, 8(1).
Huang, B. et al. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, 2, 680-682.
Lorenzetti, A. P. R. et al. (2016) PlanTE-MIR DB: a database for transposable element- related microRNAs in plant genomes. Functional & Integrative Genomics, 1-8.
Maracaja-Coutinho, V. et al. (2019), Chapter 10: Noncoding RNAs Databases: Current Status and Trend, Book: Computational Biology of Non-Coding RNA: Methods and Protocols, Springer New York, 1th edition.
Okamura, K. et al. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila, Cell, 89-100.
Paschoal, A. R. et al. (2012) Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA Biology, 274-282.
Qu, Z. and Adelson, D. (2012) Evolutionary conservation and functional roles of ncRNA, Frontiers in Genetics, 3, 205.
Ruby, J. G. et al. (2007) Intronic microRNA precursors that bypass Drosha processing, Nature, 448, 83.
Bonnet, E. et al. (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics, Bioinformatics, 26, 1566-1568.
Budak, H. and Akpinar, B. (2015) Plant miRNAs: biogenesis, organization and origins, Functional & Integrative Genomics, 15, 523-531.
Dai, X. et al. (2018) psRNATarget: a plant small RNA target analysis server (2017 release), Nucleic Acids Research.
Das, S. et al. (2018) miRwayDB: a database for experimentally validated microRNA- pathway associations in pathophysiological conditions. Database (Oxford). 2018: bay023.
Fonseca B., Domingues D., Paschoal AR. mirtronDB: a mirtron knowledge base. Bioinformatics. btz153. doi: 10.1093/bioinformatics/btz153.
Gallart, A. et al. (2015) GREENC: a Wiki-based database of plant lncRNAs. Nucleic Acids Research, 44, D1161-D1166.
Griffiths-Jones, S. et al. (2006) miRBase: microRNA sequences, targets and gene nomenclature, Nucleic Acids Research, 34, D140-D144.
Grzegorz, R. et al. (2018) Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods, Scientific Reports, 8(1).
Huang, B. et al. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences, Bioinformatics, 2, 680-682.
Lorenzetti, A. P. R. et al. (2016) PlanTE-MIR DB: a database for transposable element- related microRNAs in plant genomes. Functional & Integrative Genomics, 1-8.
Maracaja-Coutinho, V. et al. (2019), Chapter 10: Noncoding RNAs Databases: Current Status and Trend, Book: Computational Biology of Non-Coding RNA: Methods and Protocols, Springer New York, 1th edition.
Okamura, K. et al. (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila, Cell, 89-100.
Paschoal, A. R. et al. (2012) Non-coding transcription characterization and annotation: A guide and web resource for non-coding RNA databases. RNA Biology, 274-282.
Qu, Z. and Adelson, D. (2012) Evolutionary conservation and functional roles of ncRNA, Frontiers in Genetics, 3, 205.
Ruby, J. G. et al. (2007) Intronic microRNA precursors that bypass Drosha processing, Nature, 448, 83.
Publicado
26/06/2019
Como Citar
DA FONSECA, Bruno Henrique Ribeiro; DOMINGUES, Douglas Silva; PASCHOAL, Alexandre Rossi.
mirtronDB: a mirtron knowledge base. In: CONCURSO DE TESES E DISSERTAÇÕES (CTD), 32. , 2019, Belém.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2019
.
ISSN 2763-8820.
DOI: https://doi.org/10.5753/ctd.2019.6340.
