RPGeNet

RPGeNet maps the interactome of genes associated with inherited retinal dystrophies to support identification of potential causative genes and assignment of novel candidates to retinal or cellular pathways.

Key Features:

• Interaction data integration: Integrates protein–protein interaction data from STRING, BioGRID, and PPaxe.
• Retina-specific expression and variants: Incorporates retina-specific expression data and associated genetic variant annotations.
• Graph database (Neo4j): Stores the integrated interactome in a Neo4j graph database to handle complex relationships.
• Querying and scalability: Provides novel querying methods and improved query performance for extensive interactome datasets.
• Causative gene interactome mapping: Maps interactions among known causative genes of inherited syndromic and non-syndromic retinal dystrophies to facilitate candidate discovery.

Scientific Applications:

• Candidate gene discovery: Prioritizes and identifies potential new causative genes for Retinitis Pigmentosa and other inherited retinal dystrophies.
• Pathway assignment: Assigns novel candidate genes to retinal or cellular pathways based on network context.
• Unsolved patient research: Supports genetic and clinical research addressing the ~30% of retinal dystrophy patients for whom causative genes remain unidentified.
• Integrative network analysis: Enables combined analysis of protein–protein interactions, retina expression, and variant data to infer mechanistic relationships among genes.

Methodology:

Aggregates protein–protein interaction data from STRING, BioGRID, and PPaxe with retina-specific expression and genetic variant annotations and stores the integrated interactome in a Neo4j graph database to enable advanced querying.