PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs

文献类型： 外文期刊

第一作者： Jin, Jingjing

作者： Jin, Jingjing;Lu, Peng;Xu, Yalong;Li, Zefeng;Cao, Peijian;Yu, Shizhou;Liu, Jun;Wang, Huan;Chua, Nam-Hai;Chua, Nam-Hai

作者机构：

期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：16.971； 五年影响因子：15.542 ）

ISSN： 0305-1048

年卷期： 2021 年 49 卷 D1 期

页码：

收录情况： SCI

摘要： Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with little or no protein coding potential. The expanding list of lncRNAs and accumulating evidence of their functions in plants have necessitated the creation of a comprehensive database for lncRNA research. However, currently available plant lncRNA databases have some deficiencies, including the lack of lncRNA data from some model plants, uneven annotation standards, a lack of visualization for expression patterns, and the absence of epigenetic information. To overcome these problems, we upgraded our Plant Long noncoding RNA Database (PLncDB, http://plncdb. tobaccodb.org/), which was based on a uniform annotation pipeline. PLncDB V2.0 currently contains 1 246 372 lncRNAs for 80 plant species based on 13 834 RNA-Seq datasets, integrating lncRNA information from four other resources including EVLncRNAs, RNAcentral and etc. Expression patterns and epigenetic signals can be visualized using multiple tools (JBrowse, eFP Browser and EPexplorer). Targets and regulatory networks for lncRNAs are also provided for function exploration. In addition, PLncDB V2.0 is hierarchical and user-friendly and has five builtin search engines. We believe PLncDB V2.0 is useful for the plant lncRNA community and data mining studies and provides a comprehensive resource for data-driven lncRNA research in plants.

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