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