PRP

PRP integrates curated regulatory genomics datasets for plants to enable analysis of transcriptional, epigenetic, and small RNA–mediated regulation across genomes.

Key Features:

• Regulatory Search Engine: Consolidates analytical outputs and genomic tracks for regulators including transcription factors and small RNAs (sRNA/miRNAs).
• Genome Browser: Provides integrated visualization of genomic features, tracks, and analysis results.
• Analytical Capabilities: Analyzes transcription factors, sRNA/miRNAs, spot-specific DNA methylation patterns, gene expression profiles, interactions, and pathway annotations.
• RdDM Regulation Insights: Identifies potential RNA-directed DNA Methylation (RdDM) regulatory associations.
• Enrichment Analysis and Visualization: Performs enrichment analyses and generates plots for functional interpretation of regulatory elements and gene sets.
• Graph Database Utilization: Represents and visualizes regulatory networks using the Neo4j graph database to reveal relationships and long-range interactions.
• Processed Data Content: Hosts 571 GB of processed data across Arabidopsis thaliana, Oryza sativa subsp. japonica, Zea mays, and Glycine max.

Scientific Applications:

• Regulatory network analysis: Enables integrated study of plant regulatory networks combining transcription factors, epigenetic marks, and small RNAs.
• Epigenetic regulation and RdDM: Supports analysis of DNA methylation, histone modifications, and RNA-directed DNA Methylation in plants.
• Gene expression and pathway analysis: Facilitates linking gene expression profiles with pathways and Gene Ontology annotations.
• Comparative and species-specific studies: Supports analyses across Arabidopsis thaliana, Oryza sativa subsp. japonica, Zea mays, and Glycine max.

Methodology:

Integrates curated datasets from published sources including RNA sequencing, methylome analysis, sRNA/miRNA sequencing, histone modifications, repeats, gene ontology annotations, digital gene expression profiles, and characterized pathways; employs the Neo4j graph database for network representation and provides enrichment analysis, visualization, and genome browser–based integrated visualization.