WPMIAS

WPMIAS identifies and validates plant microRNA (miRNA)-target mRNA interactions using whole-degradome sequencing data to confirm mRNA cleavage events and construct degradome-based regulatory networks.

Key Features:

• User-submitted degradome data analysis: Accepts and integrates user-provided degradome datasets for validation of predicted miRNA-target interactions.
• Pre-loaded degradome repository: Includes 274 plant degradome datasets covering 64 plant species and approximately 200 cDNA libraries for comparative and reference analyses.
• Validation of MTIs: Uses whole-degradome sequencing evidence to detect mRNA cleavage sites indicative of miRNA-target interactions (MTIs).
• Degradome-based miRNA regulatory networks (MRNs): Constructs MRNs from validated MTIs to represent regulatory relationships mediated by miRNAs.
• Support for other small RNAs: Analyzes cleavage directed by other small RNAs including 21-nt phased siRNAs (phasiRNAs) and natural antisense siRNAs (nat-siRNAs).
• Comprehensive miRNA-target mapping: Generates miRNA-target maps reporting cleavage signals and comparative patterns across datasets and species.

Scientific Applications:

• MTI validation in plants: Confirms predicted miRNA-target mRNA interactions by direct observation of degradome-supported cleavage sites.
• Discovery of miRNA-mediated pathways: Enables identification of regulatory pathways and interactions relevant to plant development, stress responses, and adaptation.
• Regulatory network analysis: Facilitates reconstruction and analysis of degradome-based miRNA regulatory networks to study gene regulatory relationships.
• Small RNA cleavage studies: Supports investigation of phasiRNA- and nat-siRNA-directed mRNA cleavage alongside miRNA activity.

Methodology:

Validates predicted MTIs by analyzing whole-degradome sequencing data to detect mRNA cleavage events, integrates user-submitted and pre-loaded degradome datasets, and constructs degradome-based miRNA regulatory networks from validated MTIs.