ReactomeGSA

ReactomeGSA performs multi-omics comparative pathway analysis by providing an R client to the Reactome Analysis System that maps transcriptomics, proteomics and single-cell RNA sequencing (scRNA-seq) data across species onto the Reactome pathway database and integrates ExpressionAtlas and Single Cell ExpressionAtlas datasets for cross-species pathway interpretation.

Key Features:

• R client: Provides an R client interface to the Reactome Analysis System for programmatic access.
• Multi-Omics Integration: Handles and integrates transcriptomics and proteomics datasets within a common pathway framework.
• scRNA-seq Support: Explicitly supports single-cell RNA sequencing (scRNA-seq) data for pathway-level analysis.
• Cross-Species Mapping: Automatically maps data from different species into a unified pathway space for comparative analysis.
• Reactome Pathway Database: Uses the Reactome pathway database for pathway mapping, visualization, interpretation, and analysis.
• Integration with Public Databases: Integrates public datasets from ExpressionAtlas and Single Cell ExpressionAtlas to augment analyses.

Scientific Applications:

• Comparative multi-omics pathway analysis: Enables biomedical studies that require integrating diverse transcriptomics, proteomics, and scRNA-seq datasets across species to interpret pathway-level effects.
• B cell and tumor immunology example: Has been used to compare B cell–rich and B cell–poor human cancer samples, revealing a lack of NFkappaB activation in certain lung adenocarcinoma samples potentially linked to tumor-associated IgG+ plasma cell subsets identified by scRNA-seq.

Methodology:

Maps multi-omics datasets onto the Reactome pathway framework, aligns data from different species and omics technologies into a common analytical space, and operates via an R client interfacing with the Reactome Analysis System.