BridgeDbR

BridgeDbR integrates BridgeDb identifier mapping and PathVisio-based pathway analysis into R to support functional genomics and pathway-level interpretation of molecular data.

Key Features:

• Identifier mapping with BridgeDb: Integrates BridgeDb functions and identifier mapping databases into R for systematic conversion between gene, protein, and metabolite identifiers.
• Integration with scripting languages: Supports invocation from scripting environments such as R, Python, and Perl to run pathway analysis workflows.
• Pathway analysis capabilities: Supports creating and editing biological pathways, visualizing experimental data on pathways, performing statistical analyses, and exporting results as image files.
• Support for multiple pathway sources: Enables use of pathways from WikiPathways or user-provided pathway files for analysis.
• Automation of repetitive tasks: Provides automation for repeated visualization and analysis steps common in large-scale genomic studies.
• PathVisio connectivity: Uses the PathVisioRPC XML-RPC interface and RPathVisio to connect scripting environments with PathVisio for pathway manipulation and visualization.

Scientific Applications:

• Gene expression analysis: Applied to analysis of gene expression datasets, including datasets from NCBI GEO, for pathway-level interpretation.
• Functional analysis of differential expression: Supports functional interpretation of differentially expressed genes or proteins via pathway visualization and statistics.
• Case example: Has been used to analyze transcriptional responses in tumour-bearing mice treated with cyclophosphamide.

Methodology:

Integrates BridgeDb identifier mapping databases into R and employs the PathVisioRPC XML-RPC interface (and RPathVisio) to connect scripting languages with PathVisio for pathway visualization and statistical analysis.