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

Area of Science:

• Plant molecular biology
• Genomics
• Bioinformatics

Background:

• Non-coding RNAs (ncRNAs) are crucial regulators of protein-coding gene expression.
• Existing gene expression databases lack comprehensive ncRNA data.
• Understanding ncRNA expression patterns is vital for plant science.

Purpose of the Study:

• To develop a comprehensive expression atlas for rice ncRNAs.
• To provide tools for analyzing ncRNA co-expression and tissue specificity.
• To facilitate research on ncRNA-mediated gene regulation in rice.

Main Methods:

• Construction of the RiceNCexp database using 491 RNA-seq and 274 small RNA (sRNA)-seq datasets.
• Integration of data for four ncRNA types: lncRNAs, PHAS genes, miRNAs, and phasiRNAs.
• Development of a tau-based tool for tissue-specific ncRNA mining and co-expression analysis.

Main Results:

• RiceNCexp hosts expression data for rice ncRNAs across 22 tissues/organs.
• The atlas enables robust co-expression analysis between ncRNAs and protein-coding genes.
• 116 paired RNA-seq and sRNA-seq libraries support reliable co-expression analysis.

Conclusions:

• RiceNCexp is a valuable, user-friendly resource for rice ncRNA research.
• The atlas enhances the study of ncRNA functions and regulatory networks in rice.
• Accessible at https://cbi.njau.edu.cn/RiceNCexp/, it supports diverse plant genomics studies.