植物环状RNA：一个关于植物环状RNA的综合数据库。

PlantCircRNA: a comprehensive database for plant circular RNAs.

作者信息

He Shutian, Bing Jianhao, Zhong Yang, Zheng Xiaoyang, Zhou Ziyu, Wang Yifei, Hu Jiming, Sun Xiaoyong

机构信息

Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China.

出版信息

Nucleic Acids Res. 2025 Jan 6;53(D1):D1595-D1605. doi: 10.1093/nar/gkae709.

DOI:10.1093/nar/gkae709

PMID:39189447

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11701686/

Abstract

Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.

摘要

环状RNA（circRNAs）是最近发现的新型调控非编码RNA。虽然它们存在于许多真核生物中，但对植物环状RNA的研究却很有限。我们开发了PlantCircRNA（https://plant.deepbiology.cn/PlantCircRNA/）来填补这一空白。PlantCircRNA的两个最重要的特点是：（i）它基于39245个RNA测序样本整合了94种植物的环状RNA；（ii）它导入了原始的AtCircDB和CropCircDB数据库。我们人工整理了已发表文章中的所有环状RNA，并将它们导入数据库。此外，我们还在数据库中添加了组织以及非生物胁迫的详细信息。为了帮助用户理解这些环状RNA，该数据库包括一个用于衡量其一致性的检测分数和一个遵循最近为真核生物提出的指导原则的命名系统。最后，我们为用户开发了一个综合平台，用于可视化、分析和下载特定环状RNA的数据。这个资源将成为植物环状RNA的家园，并为科学界提供对这些神秘分子前所未有的见解。