PINA

PINA provides comprehensive analysis and annotation of protein-protein interaction networks across six model organisms by integrating unified, non-redundant protein-protein interaction data from six manually curated public databases.

Key Features:

• Coverage: Protein-protein interaction networks for six model organisms.
• Data integration: Unified, non-redundant interactome assembled from six manually curated public databases.
• Network operations: Built-in tools for network construction, filtering, analysis, and visualization.
• Interaction module collections: Multiple collections of interaction modules identified using various clustering approaches across the entire interactome.
• Module annotation: Modules annotated with enriched Gene Ontology terms, KEGG pathways, Pfam domains, and chemical and genetic perturbation signatures from MSigDB.
• Module enrichment analysis: Module enrichment analysis tool alongside a simple query function for interrogating modules.

Scientific Applications:

• Systems-level network analysis: Exploration of protein interactions at the systems level to reveal molecular network organization.
• Functional module discovery: Identification and characterization of interaction modules linked to biological processes and molecular functions via GO, KEGG, and Pfam annotations.
• Pathway and perturbation interpretation: Detection of significant biological themes or pathways and interpretation of chemical and genetic perturbations using MSigDB annotations.
• Comparative analysis: Comparative network and module analysis across six model organisms.

Methodology:

PINA integrates PPI data from six manually curated public databases into a unified, non-redundant interactome, identifies interaction modules using multiple clustering approaches, annotates modules with enriched Gene Ontology terms, KEGG pathways, Pfam domains and MSigDB chemical and genetic perturbation signatures, and provides module enrichment analysis along with network construction, filtering, analysis and visualization tools.