PathwayMatcher

PathwayMatcher maps biomedical and multiomics data to Reactome pathways at proteoform resolution, accounting for isoforms, posttranslational modifications, and protein–protein interactions to preserve proteoform-specific states during pathway analysis.

Key Features:

• Proteoform-Centric Network Construction: Integrates proteoforms—protein isoforms with specific posttranslational modifications—into the network model to represent proteoform-specific states.
• Reactome-Based Networks: Leverages the Reactome knowledge base to construct pathway and interaction networks.
• Multiomics Data Support: Processes diverse omics data types as input for pathway analyses.
• Proteoform-Level Specificity: Distinguishes interactions between different forms of the same protein to enable multiple levels of granularity.
• Output of Reactions, Subnetworks, and Pathways: Produces detailed outputs including affected biochemical reactions, subnetworks, and pathways.
• Cypher Querying and Summary Statistics: Uses Cypher language queries to extract pathway mappings and summary statistics from the constructed network.

Scientific Applications:

• Proteoform-Resolved Pathway Mapping: Maps experimental datasets to pathway components at proteoform resolution.
• Proteoform Influence on Pathway Dynamics: Enables analysis of how different isoforms and posttranslational modifications affect pathway behavior.
• Gene Expression, Protein Interaction, and Disease Studies: Applies to studies of gene expression, protein–protein interactions, and disease mechanisms where isoform- and modification-specific roles are relevant.
• Multiomics Integration: Integrates multiple omics datasets into a pathway context for comprehensive analysis.

Methodology:

Constructs a network based on Reactome that includes documented isoform and modification statuses of proteins and queries this network using Cypher language queries to extract pathway mappings and summary statistics, accepting diverse omics data types.