PathRings

PathRings visualizes Reactome metabolic and signaling pathways as compound graphs to integrate and interpret genomic, transcriptomic, and proteomic data across species.

Key Features:

• Comprehensive Visualization: Integrates metabolic and signaling pathways from Reactome into a unified compound graph representation that supports comparative analyses across multiple species or user-defined inputs.
• Color-Coded Highlighting: Applies color-coding to highlight genes and pathways affected by input data (e.g., gene expression), enabling rapid visual identification of patterns.
• Dynamic Multi-View Management: Constructs incremental multi-view visualizations that decompose complex analytical tasks and automate multi-view management to reflect analytical workflows.
• Scalability for Comparative Analysis: Scales to large experimental datasets mapped to Reactome pathways and supports comparative analyses over larger datasets.
• Visual Exploration Provenance: Preserves visual exploration provenance by maintaining overviews of the impact of gene expression data on all pathways while enabling drill-down into detailed pathway visualizations.

Scientific Applications:

• Pathway-centric data interpretation: Mapping genomic, transcriptomic, and proteomic datasets onto Reactome metabolic and signaling pathways for interpretation of large-scale experiments.
• Comparative genomics and systems biology: Cross-species pathway analysis to support comparative genomics and systems biology investigations.
• Hypothesis generation from expression data: Facilitating generation of testable hypotheses through color-coded pattern recognition and incremental visual exploration of gene expression data.

Methodology:

Leverages the Reactome pathway database and presents pathways as compound graphs with dynamic multi-view visualizations that support incremental exploration and interaction among multiple dataset visualizations.