PlaNC-TE：植物中非编码 RNA 和转座子的综合知识库。
PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants.
机构信息
Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Federal University of Technology - Paraná, Cornélio Procópio, PR, Brazil.
Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
出版信息
Database (Oxford). 2018 Jan 1;2018:1-7. doi: 10.1093/database/bay078.
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.
转座元件 (TEs) 在真核物种的遗传变异性中起着至关重要的作用。在植物中，它们可能占总基因组的 90%。非编码 RNA (ncRNAs) 已知可以控制基因表达和调控。尽管已知 ncRNAs 与 TEs 之间存在关系，但要获得已测序基因组的组织化数据并不容易。在这项研究中，我们描述了 PlaNC-TE（http://planc-te.cp.utfpr.edu.br），这是一个用户友好的门户，通过整合和分析植物 ncRNA-TE 数据创建了一个知识库。我们在 40 种植物基因组中总共鉴定出了 14350 个 ncRNA 和 TEs 之间的重叠。该数据库允许用户浏览、搜索和下载所有分析的 ncRNA 和 TE 数据。总的来说，PlaNC-TE 不仅组织了数据并提供了关于植物中 ncRNA 和 TEs 之间关系的见解，还有助于改进基因组注释策略。此外，这是第一个提供资源以广泛研究植物中 TEs 和 ncRNAs 涉及的功能和机制的数据库。
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