RiceNCexp

RiceNCexp compiles and analyzes expression profiles of non-coding RNAs (ncRNAs) in rice, integrating RNA-seq and sRNA-seq datasets to characterize long non-coding RNAs (lncRNAs), PHAS genes, microRNAs (miRNAs), and phased small interfering RNAs (phasiRNAs) across multiple tissues.

Key Features:

• Comprehensive ncRNA Coverage: Includes lncRNAs, PHAS genes, miRNAs, and phasiRNAs with expression profiles across 22 rice tissues and organs.
• Tissue-Specificity Mining: Implements a tau-based metric to identify tissue-specific ncRNAs.
• Co-expression Analysis: Performs correlation analysis among ncRNAs and between ncRNAs and protein-coding genes using 116 paired RNA-seq and sRNA-seq libraries from matched experimental conditions.

Scientific Applications:

• Regulatory Network Analysis in Rice: Supports investigation of ncRNA–gene interactions, tissue-specific regulation, and developmental processes in rice.

Methodology:

RiceNCexp integrates large-scale RNA-seq and sRNA-seq datasets to quantify ncRNA expression, applies tau-based calculations to assess tissue specificity, and computes co-expression relationships using paired transcriptomic and small RNA libraries.