PtncRNAdb

PtncRNAdb catalogs transfer RNA-derived non-coding RNAs (tncRNAs) from plants and provides a curated dataset and analytical resources to study their sequences, secondary structures, differential expression, and predicted targets.

Key Features:

• Extensive Data Repository: Contains over 4.8 million tncRNA entries derived from approximately 2,500 single-end small RNA-seq libraries across six model plants: Arabidopsis thaliana, Cicer arietinum, Zea mays, Oryza sativa, Medicago truncatula, and Solanum lycopersicum.
• Sequence Querying (BLASTN): Provides BLASTN-based sequence querying against PtncRNAdb entries.
• Data Visualization: Integrates Highcharts for statistical visualization of tncRNA datasets.
• Differential Expression (DE tncRNAs): Includes a 'DE tncRNAs' module for exploration of differentially expressed tncRNAs under various conditions.
• Secondary Structure and Target Prediction: Supplies predicted secondary structures of tncRNAs and putative target predictions.
• Interactive Networks and Target Enrichment Analysis: Offers interactive networks to support target enrichment analysis and links to related publications.

Scientific Applications:

• Gene regulation studies: Facilitate investigation of tncRNA roles in post-transcriptional gene regulation.
• Development and stress-response research: Enable analysis of tncRNA involvement in plant development and stress tolerance pathways.
• Functional network and target analysis: Support target enrichment and interaction-network analyses to infer functional relationships of tncRNAs.

Methodology:

Compiled from single-end small RNA-seq libraries; sequence querying via BLASTN; predicted tncRNA secondary structures and putative targets; differential expression assessed via the 'DE tncRNAs' module; interactive network construction for target enrichment analysis; statistical visualization implemented with Highcharts.