RiceNCexp: A Resource for Rice Non-coding RNA Co-Expression Atlas Based on Massive RNA-seq and Small-RNA seq Data

J Exp Bot. 2022 Jun 28;erac285. doi: 10.1093/jxb/erac285. Online ahead of print.


Non-coding RNAs (ncRNAs) play important roles in regulating expression of protein-coding genes. Although gene expression databases have emerged timely, however, the comprehensive expression database for ncRNAs is still lacking. Herein, we constructed a rice non-coding RNA co-expression atlas (RiceNCexp), based on 491 RNA-seq and 274 sRNA-seq datasets. RiceNCexp hosts four types of ncRNAs including lncRNA, PHAS gene, microRNA and phasiRNA. 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 small RNA-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 h ttps://cbi.njau.edu.cn/RiceNCexp/.

Keywords: RNA-seq; co-expression; database; non-coding RNA; rice; sRNA-seq.