graphite

graphite reconstructs gene/protein networks from pathway topology to enable topology-aware gene set analysis.

Key Features:

• Pathway topology integration: Incorporates pathway topology as a central feature to preserve signaling relationships during network reconstruction.
• Entity resolution: Distinguishes protein complexes and gene family members as separate biological entities in network representations.
• Chemical compound handling: Sensibly excludes chemical compounds from final gene/protein network representations.
• Database integration: Integrates pathway information from four major pathway databases for comprehensive coverage.
• Biologically-driven rules: Interprets pathway data using biologically-driven rules to guide network simplification.
• Network reconstruction: Converts complex pathway topologies into simplified gene-gene or protein-protein networks where nodes represent genes or proteins.
• Topological analysis support: Provides network outputs formatted to enable three recently proposed topological analysis methodologies.
• Bioconductor integration: Implements these capabilities as a Bioconductor package for use within the R ecosystem.

Scientific Applications:

• Topology-aware gene set analysis: Supports gene set analyses that require pathway topology information for interpretation.
• Pathway topological methods: Enables application of topological analysis methods that assess pathway structure and signal propagation.
• Network-based pathway analysis: Provides reconstructed gene-gene networks as a uniform resource for pathway analyses.
• Representation of complex entities: Facilitates study of protein complexes and gene family contributions within pathway-derived networks.

Methodology:

Integrates pathway information from four major databases and applies biologically-driven rules to convert complex pathway topologies—resolving protein complexes and gene family members and excluding chemical compounds—into simplified gene/protein networks provided as gene-gene networks and made available to three recently proposed topological analysis methods.