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

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 (RiceN...

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Bibliographic Details
Published in:Journal of experimental botany 2022-10, Vol.73 (18), p.6068-6077
Main Authors: Zhang, Baoyi, Fei, Yuhan, Feng, Jiejie, Zhu, Xueai, Wang, Rui, Xiao, Hanqing, Zhang, Hongsheng, Huang, Ji
Format: Article
Language:English
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Summary: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/.
ISSN:0022-0957
1460-2431
DOI:10.1093/jxb/erac285