Zhou Bailing, Zhao Huiying, Yu Jiafeng, Guo Chengang, Dou Xianghua, Song Feng, Hu Guodong, Cao Zanxia, Qu Yuanxu, Yang Yuedong, Zhou Yaoqi, Wang Jihua
Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China.
College of Physics and Electronic Information, Dezhou University, Dezhou, China.
Methods Mol Biol. 2019;1933:431-437. doi: 10.1007/978-1-4939-9045-0_27.
Plant long noncoding RNAs (lncRNAs) play important functional roles in various biological processes. Most databases deposit all plant lncRNA candidates produced by high-throughput experimental and/or computational techniques. There are several databases for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases, or interactions). Thus, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to May 1, 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer, and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species, including 428 plant lncRNAs from 44 plant species. Compared to PLNIncRBase, our dataset does not contain any lncRNAs from microarray and deep sequencing. Moreover, 40% of entries contain new information (interaction and additional information from NCBI and Ensembl). The database allows users to browse, search, and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs .
植物长链非编码RNA（lncRNAs）在各种生物学过程中发挥着重要的功能作用。大多数数据库存储了通过高通量实验和/或计算技术产生的所有植物lncRNA候选物。有几个用于实验验证的lncRNAs的数据库。然而，这些数据库规模较小（仅包含几百个lncRNAs）且重点各异（植物、疾病或相互作用）。因此，我们通过整理经低通量实验验证的lncRNAs（截至2016年5月1日），并整合特定数据库（lncRNAdb、LncRANDisease、Lnc2Cancer和PLNIncRBase）以及先前未涵盖的其他功能和疾病特异性信息，建立了EVLncRNAs。EVLncRNAs的当前版本包含来自77个物种的1543个lncRNAs，其中包括来自44个植物物种的428个植物lncRNAs。与PLNIncRBase相比，我们的数据集中不包含任何来自微阵列和深度测序的lncRNAs。此外，40%的条目包含新信息（来自NCBI和Ensembl的相互作用及其他信息）。该数据库允许用户浏览、搜索、下载以及提交经实验验证的lncRNAs。该数据库可在http://biophy.dzu.edu.cn/EVLncRNAs获取。
