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pathway-mapping

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Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with correct background-set construction and honest interpretive ceilings. Use when interpreting differential metabolites or an untargeted LC-MS feature table in pathway context, choosing ORA vs MSEA vs mummichog vs topology, or setting the reference/background set. For annotation confidence levels feeding ORA see metabolomics/metabolite-annotation; for gene-set concepts see pathway-analysis/go-enrichment and pathway-analysis/gsea; for joint gene+metabolite pathways see multi-omics-integration/mofa-integration.

When to use

• Interpreting differential metabolites in pathway context
• Analyzing untargeted LC-MS feature tables
• Choosing between ORA, MSEA, mummichog, and topology methods
• Setting reference or background sets for enrichment
• Mapping identified compounds to pathways
• Predicting pathway activity from raw m/z peaks
• Analyzing network diffusion for enzyme and reaction links

When not to use

• Metabolite annotation confidence levels
• Gene-set concepts and GO enrichment
• Joint gene and metabolite pathway integration

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