CPA - Comparative Pathway Analyzer

CPA - Comparative Pathway Analyzer compares metabolic reaction content between two organism sets and visualizes differences on KEGG pathway maps to support comparative metabolic network analysis and interpretation of phenotypic variation.

Key Features:

• Comparative Analysis: Calculates and displays differences in metabolic reaction content between two sets of organisms.
• Visualization on KEGG Pathway Maps: Maps reaction differences onto Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway maps for standardized visualization.
• Hierarchical Clustering Methods: Applies hierarchical clustering to group organisms and assist definition of organism sets for comparative analyses.
• Simultaneous Visualization: Supports concurrent visualization of reaction content from multiple organisms for direct comparison.
• Custom Data Uploads: Integrates KEGG annotation data and accepts user-uploaded custom annotation data.

Scientific Applications:

• Systems Biology: Analyzes organism metabolic networks to study system-level metabolic differences.
• Comparative Genomics: Compares metabolic pathway content across genomes to identify conserved and divergent reactions.
• Evolutionary Relationships: Provides insight into evolutionary relationships by comparing presence/absence patterns of metabolic reactions across organisms.
• Metabolic Capability Identification: Identifies unique metabolic capabilities present in specific organisms or groups.
• Genotype–Phenotype Mapping: Associates genetic variation with phenotypic metabolic traits by comparing reaction content.
• Disease and Functional Metabolism Studies: Elucidates metabolic underpinnings of specific biological functions or diseases through pathway comparison.

Methodology:

Computes reaction-content differences between organism sets, applies hierarchical clustering to define organism groupings, and projects results onto KEGG pathway maps for visualization.