IntAct App

IntAct App visualizes and analyzes molecular interaction networks curated in the IntAct database to enable exploration of protein, gene, RNA, and chemical interactions including mutation-specific evidence.

Key Features:

• Network Construction: Constructs interaction networks by querying molecules via multiple identifier fields and optionally expanding to include all interacting partners.
• Entity Representation: Represents proteins, genes, RNA, and chemicals as nodes and encodes interaction evidence as edges.
• Visualization Modes: Provides three visualization modes: a basic interaction-only view, an evidence-focused view showing individual pieces of interaction data, and a mutation-focused view emphasizing interactions involving mutated protein versions.
• Filtering and Evidence Retrieval: Supports filtering networks by specified criteria and retrieval of detailed interaction and molecule metadata and evidence records.
• Automation Support: Exposes functionality via Cytoscape's command-line interface for scripted and batch operations.

Scientific Applications:

• Interaction network analysis: Enables identification of key interaction partners and network topology relevant to cellular processes and disease mechanisms.
• Mutation impact studies: Supports analysis of interactions involving mutated protein versions to assess effects on protein function.
• Proteomics and functional genomics: Facilitates integration and interpretation of proteomics and functional genomics data within interaction contexts.
• Evidence assessment: Allows evaluation of interaction reliability and context using evidence-level visualizations.

Methodology:

Imports molecular interaction records from the IntAct database into Cytoscape 3, maps molecules (proteins, genes, RNA, chemicals) to nodes and interaction evidence to edges, retains mutation-specific evidence, and exposes operations via the Cytoscape command-line interface.