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kegg-analysis

Orchestrates KEGG bioinformatics workflows for pathway enrichment, drug targets, and cross-species comparison.

3.4k|487|Updated Jul 25, 2025
Search Tags:#mcp#bioinformatics#gene analysis#pathway enrichment#kegg#drug targets#cross-species comparison
One-click install
npx skills add https://github.com/davepoon/buildwithclaude --skill kegg-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-analysis
Source: https://github.com/davepoon/buildwithclaude/tree/main/plugins/kegg-mcp-server/skills/kegg-analysis
Command: npx skills add https://github.com/davepoon/buildwithclaude --skill kegg-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Turning raw gene lists, drug names, or pathway IDs into meaningful biological insights requires chaining many KEGG database lookups by hand. This Skill automates those multi-step analytical pipelines so researchers get ranked pathways, drug mechanisms, and conservation analyses without manual database navigation.

Core Features & Use Cases

  • Pathway Enrichment Analysis: Maps gene lists to KEGG pathways, aggregates hits, and ranks pathways with biological context.
  • Drug Target Investigation: Resolves drug entries, identifies targets and interactions, and synthesizes mechanism-of-action summaries.
  • Cross-Species Comparison: Compares metabolic pathways across organisms using ortholog mapping and metabolite pool analysis.
  • Use Case: A researcher submits antioxidant genes (SOD1, SOD2, CAT, GPX1, PRDX1) and receives a ranked report showing enrichment in Peroxisome, Ferroptosis, and neurodegeneration pathways with explanatory biological context.

Quick Start

Ask Claude to analyze a gene list for pathway enrichment in a specific organism, for example by requesting pathway enrichment analysis of BRCA1, TP53, and EGFR in human.

Frequently Asked Questions about kegg-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I perform KEGG pathway enrichment analysis on a gene list?▼

Provide your gene symbols and target organism, and the workflow searches each gene, retrieves pathway associations, and aggregates hits per pathway. Results are ranked by gene count with biological context explaining each pathway's significance.

How to investigate drug targets and interactions using KEGG?▼

Submit a drug name like metformin and the workflow finds the KEGG drug entry, retrieves targets and classification, maps target genes to pathways, and screens drug-drug interactions. It then synthesizes a mechanism-of-action summary.

Can I compare metabolic pathways across different species in KEGG?▼

Yes, provide a pathway ID and organism list such as human, E. coli, and yeast. The workflow retrieves organism-specific pathway variants, identifies conserved versus species-specific enzymes via orthologs, and compares metabolite pools.

What gene identifier formats does KEGG analysis support?▼

Standard gene symbols work directly, including HGNC symbols for human genes. The convert_identifiers tool bridges UniProt, NCBI Gene, and PDB IDs when your data uses alternative identifier systems.

What are the limitations when analyzing large gene lists with KEGG?▼

For lists over 20 genes, batch processing with batch_entry_lookup is required, capped at 50 entries per call. Very large lists need multiple batched requests, and providing organism context upfront speeds up identifier resolution.

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