KEGGgraph

KEGGgraph converts KGML (KEGG XML) pathway maps from the Kyoto Encyclopedia of Genes and Genomes (KEGG) into graph models for analysis of biological networks within the R/Bioconductor environment.

Key Features:

• Parsing and Integration: Parses KGML (KEGG XML) files and transforms KEGG pathway maps into graph models while preserving manually curated pathway attributes.
• Graph Theory Representation: Represents pathway components and relations as graph structures to capture pathway topology for structural and functional analysis.
• Visualization and Analysis Functions: Provides functions to visualize and analyze pathway graphs to explore interactions and identify network components.
• R/Bioconductor Integration: Interoperates with the R/Bioconductor ecosystem for statistical computing and graphics on pathway graph objects.
• Case Study Application: Applied to analysis of human pancreatic cancer pathways to illustrate pathway-level insights into disease mechanisms.

Scientific Applications:

• Genomics: Enables mapping of genomic entities onto KEGG pathways for network-based interpretation of genomic data.
• Proteomics: Supports integration of proteomic identifiers into pathway graphs to analyze protein-level interactions and network context.
• Systems Biology: Facilitates structural and topological analysis of pathways for systems-level characterization of biological processes.
• Disease Research: Allows pathway-centric investigation of disease mechanisms, exemplified by application to pancreatic cancer pathways.
• Drug Discovery: Supports identification of pathway components and interactions relevant to therapeutic targeting and mechanism-of-action studies.
• Personalized Medicine: Enables pathway-based interpretation of molecular profiles to inform individualized biological hypotheses.

Methodology:

Parses KGML (KEGG XML) files to convert KEGG's manually curated pathway maps into graph models while retaining pathway attributes, and integrates those graph objects with R/Bioconductor for downstream statistical analysis and graphics.