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EVLncRNAs 3.0:一个更新的综合数据库,用于手动管理的功能性长非编码RNA,并通过低通量实验进行验证。

EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments.

发表日期:2023 Nov 11
作者: Bailing Zhou, Baohua Ji, Congcong Shen, Xia Zhang, Xue Yu, Pingping Huang, Ru Yu, Hongmei Zhang, Xianghua Dou, Qingshuai Chen, Qiangcheng Zeng, Xiaoxin Wang, Zanxia Cao, Guodong Hu, Shicai Xu, Huiying Zhao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
来源: NUCLEIC ACIDS RESEARCH

摘要:

长非编码 RNA (lncRNA) 已成为多种生物过程和疾病的关键调节因子。虽然高通量测序已经使 lncRNA 的发现成为可能,但功能表征仍然有限。 EVLncRNA 数据库是第一个也是唯一的存储库,包含来自不同物种的所有经过实验验证的功能性 lncRNA。继 2018 年和 2021 年发布之前的版本之后,本次更新标志着一次重大扩展,从 2020 年 5 月 15 日到 2023 年 5 月 15 日,通过对近 25,000 篇出版物进行详尽的手动管理,实现了重大扩展。它涵盖了所有类别的大幅增长:功能性 lncRNA 增加了 154%,160相关疾病占 %,lncRNA 疾病关联占 186%,相互作用占 235%,结构占 138%,环状 RNA 占 234%,耐药性 lncRNA 占 235%,外泌体 lncRNA 占 4724%。更重要的是,它纳入了额外的信息,包括功能分类、详细的相互作用途径、同源lncRNA、lncRNA位置、COVID-19、相分离和类器官相关lncRNA。 Web 界面在浏览、可视化和搜索方面得到了显着改进。 ChatGPT 已针对信息提取和功能概述进行了测试,并指出了其局限性。 EVLncRNA 3.0 代表了经过实验验证的功能性 lncRNA 最广泛的资源,并将成为揭示新兴 lncRNA 功能不可或缺的平台。更新后的数据库可在 https://www.sdklab-biophysicals-dzu.net/EVLncRNAs3/ 上免费获取。© 作者 2023。由牛津大学出版社代表 Nucleic Acids Research 出版。
Long noncoding RNAs (lncRNAs) have emerged as crucial regulators across diverse biological processes and diseases. While high-throughput sequencing has enabled lncRNA discovery, functional characterization remains limited. The EVLncRNAs database is the first and exclusive repository for all experimentally validated functional lncRNAs from various species. After previous releases in 2018 and 2021, this update marks a major expansion through exhaustive manual curation of nearly 25 000 publications from 15 May 2020, to 15 May 2023. It incorporates substantial growth across all categories: a 154% increase in functional lncRNAs, 160% in associated diseases, 186% in lncRNA-disease associations, 235% in interactions, 138% in structures, 234% in circular RNAs, 235% in resistant lncRNAs and 4724% in exosomal lncRNAs. More importantly, it incorporated additional information include functional classifications, detailed interaction pathways, homologous lncRNAs, lncRNA locations, COVID-19, phase-separation and organoid-related lncRNAs. The web interface was substantially improved for browsing, visualization, and searching. ChatGPT was tested for information extraction and functional overview with its limitation noted. EVLncRNAs 3.0 represents the most extensive curated resource of experimentally validated functional lncRNAs and will serve as an indispensable platform for unravelling emerging lncRNA functions. The updated database is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/.© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.