RiceNCexp：一个基于海量 RNA-seq 和 small-RNA seq 数据的水稻非编码 RNA 共表达图谱。

RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data.

机构信息

State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.

Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing 210095, China.

出版信息

J Exp Bot. 2022 Oct 18;73(18):6068-6077. doi: 10.1093/jxb/erac285.

DOI:10.1093/jxb/erac285

PMID:35762882

Abstract

Non-coding RNAs (ncRNAs) play important roles in regulating expression of protein-coding genes. Although gene expression databases have emerged in a timely manner, a comprehensive expression database for ncRNAs is still lacking. Herein, we constructed a rice ncRNA co-expression atlas (RiceNCexp), based on 491 RNA-seq and 274 small RNA (sRNA)-seq datasets. RiceNCexp hosts four types of ncRNAs, namely lncRNAs, PHAS genes, miRNAs, and phasiRNAs. RiceNCexp provides comprehensive expression information for rice ncRNAs in 22 tissues/organs, an efficient tau-based mining tool for tissue-specific ncRNAs, and the robust co-expression analysis among ncRNAs or between ncRNAs and protein-coding genes, based on 116 pairs of RNA-seq and sRNA-seq libraries from the same experiments. In summary, RiceNCexp is a user-friendly and comprehensive rice ncRNA co-expression atlas and can be freely accessed at https://cbi.njau.edu.cn/RiceNCexp/.

摘要

非编码 RNA（ncRNAs）在调控蛋白编码基因的表达中发挥着重要作用。尽管基因表达数据库已经及时出现，但仍缺乏全面的 ncRNA 表达数据库。在此，我们构建了一个水稻 ncRNA 共表达图谱（RiceNCexp），它基于 491 个 RNA-seq 和 274 个小 RNA（sRNA）-seq 数据集。RiceNCexp 包含四种 ncRNAs，即 lncRNAs、PHAS 基因、miRNAs 和 phasiRNAs。RiceNCexp 为水稻 ncRNAs 在 22 种组织/器官中的表达提供了全面的信息，提供了基于相同实验的 116 对 RNA-seq 和 sRNA-seq 文库的组织特异性 ncRNAs 的高效 tau 挖掘工具，以及 ncRNAs 或 ncRNAs 与蛋白编码基因之间的稳健共表达分析。总之，RiceNCexp 是一个用户友好且全面的水稻 ncRNA 共表达图谱，可在 https://cbi.njau.edu.cn/RiceNCexp/ 上免费访问。