Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.
College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D98-D106. doi: 10.1093/nar/gkad1057.
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/.
长链非编码 RNA（lncRNA）已成为多种生物过程和疾病的关键调控因子。虽然高通量测序技术已经实现了 lncRNA 的发现，但功能表征仍然有限。EVLncRNAs 数据库是首个也是唯一一个专门用于存储来自不同物种的所有经过实验验证的功能性 lncRNA 的数据库。在 2018 年和 2021 年的前两次发布之后，本次更新通过对 2020 年 5 月 15 日至 2023 年 5 月 15 日的近 25000 篇文献进行详尽的手动整理，实现了重大扩展。它在所有类别中都有了实质性的增长：功能性 lncRNA 增加了 154%，相关疾病增加了 160%，lncRNA-疾病关联增加了 186%，相互作用增加了 235%，结构增加了 138%，环状 RNA 增加了 234%，耐药 lncRNA 增加了 235%，外泌体 lncRNA 增加了 4724%。更重要的是，它还增加了包括功能分类、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 等在内的更多信息。浏览、可视化和搜索的网页界面也得到了大幅改进。我们还测试了 ChatGPT 进行信息提取和功能概述的能力，并指出了其局限性。EVLncRNAs 3.0 代表了最广泛的经过实验验证的功能性 lncRNA curated 资源，将成为揭示新兴 lncRNA 功能的不可或缺的平台。更新后的数据库可在 https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/ 免费获取。
