MetENP

MetENP performs metabolite enrichment and pathway analysis to identify significant metabolites from mass spectrometry-derived measurements, compute pathway enrichment scores, map metabolites to species-specific KEGG pathways, and link metabolites to gene–enzyme information and enzymatic activities.

Key Features:

• Input data handling: Accepts metabolite names, concentrations, and associated metadata derived from high-throughput mass spectrometric methods for detection of significant metabolites.
• Enrichment analysis: Performs metabolite enrichment analysis to identify sets of metabolites enriched in experimental contrasts.
• Species-specific pathway analysis: Maps metabolites to species-specific KEGG pathways to enable organism-aware pathway interpretation.
• Pathway enrichment scores: Calculates quantitative pathway enrichment scores to measure significance of observed metabolite changes within pathways.
• Gene–enzyme and enzymatic activity annotation: Associates significantly altered metabolites with gene–enzyme information and reported enzymatic activities.
• Customizable workflow: Provides user-specified options to customize analysis parameters and selection criteria.
• KEGG coverage: Supports mapping for metabolite species that have available KEGG pathway annotations.
• Implementation: Implemented as an R package for computational analysis.

Scientific Applications:

• Biomedical research: Identifies altered metabolites and pathways to investigate normal and diseased physiological functions and disease mechanisms.
• Phenotype association: Translates raw metabolomics measurements into mechanistic hypotheses relating metabolite and pathway alterations to phenotypes.

Methodology:

Combines metabolite enrichment analysis with pathway analysis using species-specific KEGG mapping, calculates pathway enrichment scores, and links metabolites to gene–enzyme and enzymatic activity information.