pathview

pathview maps experimental data onto biological pathway graphs to integrate omics measurements with pathway structure for pathway-based interpretation of molecular mechanisms.

Key Features:

• Automated Pathway Graph Acquisition: Automatically retrieves pathway graph data required for mapping.
• Data Mapping and Integration: Parses user-supplied data files and maps experimental values onto pathway graph elements for a specified target pathway.
• Visualization Capabilities: Renders pathway graphs that incorporate mapped data to visualize biological processes and interactions.
• Integration with Analysis Tools: Integrates with other pathway and functional analysis tools to support large-scale automated analysis pipelines.

Scientific Applications:

• Omics pathway mapping: Maps genomics, transcriptomics, proteomics, and metabolomics data onto pathways for pathway-level analysis.
• Mechanistic interpretation: Visualizes experimental signals in pathway context to aid interpretation of molecular mechanisms and disease-related processes.
• Large-scale automated studies: Serves as a component in automated pipelines for high-throughput pathway-based analyses.

Methodology:

Accepts user-supplied experimental data and a specified target pathway, automatically retrieves the corresponding pathway graph data, parses the data file and maps it onto the pathway graph, and renders the integrated pathway graph visualization.