davepoon/kegg-analysis
plugins/kegg-mcp-server/skills/kegg-analysis/SKILL.md
Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration. Guides Claude through the full analytical pipeline using KEGG MCP tools.
$ install --global
skillsauthnpx skillsauth add davepoon/buildwithclaude kegg-analysisInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- kegg-analysis
- category:
- data-ai
- description:
- Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration. Guides Claude through the full analytical pipeline using KEGG MCP tools.
KEGG Bioinformatics Analysis
This skill orchestrates multi-step biological analyses using the KEGG MCP server tools. It transforms raw gene lists, drug names, or pathway IDs into structured biological insights.
When to Use This Skill
- Performing pathway enrichment analysis on a gene list
- Investigating a drug's mechanism of action, targets, and interactions
- Comparing metabolic pathways across species
- Tracing compound-reaction networks
- Mapping genes to functional modules and ortholog groups
What This Skill Does
- Identifies the analysis type from the user's input (enrichment, drug, comparison, network)
- Resolves identifiers — maps gene symbols, drug names, or pathway IDs to KEGG entries
- Retrieves cross-linked data — follows relationships across KEGG databases
- Aggregates and ranks results — counts pathway hits, scores conservation, groups by function
- Synthesizes biological context — explains significance, not just IDs
How to Use
Pathway Enrichment
Analyze these genes for pathway enrichment in human: BRCA1, TP53, EGFR, KRAS, PIK3CA
Workflow:
search_genesfor each gene in the target organism (e.g., hsa)get_gene_infoto confirm identity and get KEGG gene IDsfind_related_entriesto get pathway associations per gene- Aggregate: count how many input genes map to each pathway
get_pathway_infofor top pathwaysrender_pathway_asciifor visual context- Report ranked pathways with p-value proxy (gene count / pathway size)
Drug Target Investigation
Investigate metformin: targets, pathways, and interactions
Workflow:
search_drugsto find the KEGG drug entryget_drug_infofor targets, classification, and metabolismsearch_genesfor each target genefind_related_entriesto get target pathwaysget_drug_interactionsfor DDI screening- Synthesize mechanism-of-action summary
Cross-Species Comparison
Compare glycolysis (map00010) between human, E. coli, and yeast
Workflow:
get_pathway_infofor organism-specific variants (hsa00010, eco00010, sce00010)get_pathway_genesfor each organismget_gene_orthologsto identify conserved vs. species-specific enzymesget_pathway_compoundsto compare metabolite poolsrender_pathway_asciifor each organism- Report conservation matrix and unique adaptations
Example
User: "What pathways are enriched in this gene set: SOD1, SOD2, CAT, GPX1, PRDX1?"
Output:
Pathway Enrichment Results (Homo sapiens)
Top Pathways:
1. hsa04146 Peroxisome (4/5 genes) — organelle for fatty acid oxidation and ROS detox
2. hsa04216 Ferroptosis (3/5 genes) — iron-dependent cell death regulated by GPX
3. hsa05022 Pathways of neurodegeneration (3/5 genes) — oxidative damage in ALS, AD, PD
4. hsa00480 Glutathione metabolism (2/5 genes) — GSH-dependent antioxidant system
Biological Context:
All 5 genes encode antioxidant enzymes. The enrichment in Peroxisome
and Ferroptosis pathways reflects their central role in reactive oxygen
species (ROS) detoxification. The neurodegeneration hit is consistent
with oxidative stress as a driver of SOD1-linked ALS.
Tips
- Provide organism context (human, mouse, E. coli) for faster resolution
- Use standard gene symbols — KEGG resolves HGNC symbols for human
- For large gene lists (>20), batch with
batch_entry_lookup(max 50 per call) - Cross-reference with
convert_identifiersto bridge UniProt, NCBI Gene, or PDB IDs - Use
find_related_entriesto discover unexpected connections between databases
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