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KEGG PATHWAY is a collection of manually drawn pathway maps in the KEGG (Kyoto Encyclopedia of Genes and Genomes) resource, described on its own page as “wiring diagrams of molecular interactions, reactions and relations.” This guide is for researchers who need to read a KEGG map identifier, find the right map, understand the licence, and cite KEGG correctly. It is based on KEGG’s own pages, read 2026-11-07.
What is a KEGG pathway?
A KEGG pathway is one manually drawn map in the PATHWAY database. Each map shows molecular interactions, reactions and relations as a diagram, and the same map can be displayed in a reference form or coloured for a particular organism. PATHWAY is one of KEGG’s core databases, alongside Brite, KO (KEGG Orthology, which groups functional orthologs), Genes, Chemical, Disease, Drug and Medicus. The related tools include KEGG Mapper, Syntax, BlastKOALA and GhostKOALA. For the concept-level definition, see the KEGG dictionary entry.
The seven pathway categories
KEGG PATHWAY groups its maps into seven categories: Metabolism; Genetic Information Processing; Environmental Information Processing; Cellular Processes; Organismal Systems; Human Diseases; and Drug Development.
How to read a KEGG map ID
A map identifier is a two- to four-letter prefix followed by five digits, for example map01100. The prefix tells you what kind of map you are looking at.
| Prefix | What the map is |
|---|---|
| map | Manually drawn reference map |
| ko | Reference map highlighting KOs (KEGG Orthology entries) |
| ec | Map highlighting EC numbers |
| rn | Map highlighting reactions |
| organism code (for example hsa) | Organism-specific map, with KOs converted to gene identifiers |
| vg / vx | Virus maps |
The digits also carry meaning. Numbers beginning 011 are global maps, 012 overview maps, 013 higher-level overview maps, 010 chemical structure maps, and numbers beginning 07 are drug structure maps. So map01100 is a global map. Source: KEGG PATHWAY page, kegg.jp/kegg/pathway.html.
Who runs KEGG and what is the licence?
KEGG is developed by Kanehisa Laboratories, with collaborators at the Bioinformatics Center of Kyoto University’s Institute for Chemical Research and the Human Genome Center of the University of Tokyo’s Institute of Medical Science. The project began in 1995.
KEGG describes itself as “an original database product, copyright Kanehisa Laboratories,” offered without warranty. Its legal page distinguishes three situations:
- Academic users may use the kegg.jp website or the genome.jp mirror freely.
- Academic service providers need an academic service provider licence, which is included in the academic FTP subscription handled through pathway.jp.
- Non-academic use needs a commercial licence through Pathway Solutions. KEGG states that it is neither a public nor a publicly funded database.
Check the legal page for the terms that apply to your own use before downloading or redistributing data. Source: kegg.jp/kegg/legal.html (page dated 2024-10-01).
How to search for a pathway
- Open the KEGG PATHWAY page at kegg.jp/kegg/pathway.html.
- Use the Select prefix menu to choose the kind of map (reference, organism-specific and so on).
- Type a term into the Enter keywords box, or browse the seven categories.
- Open a map to see its diagram and linked entries.
Mapping your own gene or compound list with KEGG Mapper
KEGG Mapper Search takes a list of identifiers and shows where they fall in the pathway collection.
- Choose the search mode: Reference, hsa (human), or another organism code.
- Enter KEGG identifiers separated by spaces, tabs or new lines, or upload a file.
- Optionally tick Include “same as” objects or Include aliases (aliases apply to hsa and other organism codes).
- Choose the target: Pathway (map, hsa or organism), Brite, Module, Network or Disease.
- Run the search. Found objects are marked in red on the result.
Gene symbols are no longer supported as aliases, except official human symbols that are converted to KEGG identifiers; the page recommends using hsa gene IDs. Source: kegg.jp/kegg/mapper/search.html.
KEGG pathway analysis versus GO enrichment
People often search “KEGG pathway analysis” and “GO and KEGG enrichment” together, but they use different annotation systems. KEGG PATHWAY is a set of manually drawn maps, as described above. Gene Ontology (GO) is a separate controlled vocabulary of terms; a GO enrichment analysis tests whether genes in your list are over-represented among genes annotated to GO terms, and a KEGG pathway enrichment analysis does the same against KEGG maps. The statistics are run in enrichment software, not by KEGG itself. CASRAI has guides on several tools used for enrichment analysis: clusterProfiler, GSEA, Enrichr and DAVID.
Strengths and limits
- Strength: maps are manually drawn and organised in a documented category and ID scheme, so a map ID is a precise, citable reference point.
- Strength: the same map can be viewed in reference form or per organism, via the prefix system.
- Limit: licensing differs for academic, service-provider and commercial use, so reuse in a product or a hosted service needs a licence check.
- Limit: gene symbols are not accepted as Mapper aliases for most organisms, so identifiers must be converted to KEGG IDs first.
Related tools and background
| Resource | Relation to KEGG PATHWAY |
|---|---|
| MSigDB | Gene-set collection used in enrichment analysis |
| g:Profiler | Web tool for functional enrichment analysis |
| MetaboAnalyst | Metabolomics analysis platform |
| Systems biology overview | Background on the field that pathway maps support |
How to cite KEGG
KEGG’s own page lists these references: Kanehisa M. et al., “KEGG: biological systems database as a model of the real world,” Nucleic Acids Research 53 (2025); Kanehisa M. and Goto S., “KEGG: Kyoto Encyclopedia of Genes and Genomes,” Nucleic Acids Research 28 (2000); and Kanehisa M., Protein Science 28 (2019). Also record the map ID and the date you accessed it.
Frequently asked questions
What does the KEGG database do?
KEGG is a knowledge base from Kanehisa Laboratories with core databases for pathways, orthologs, genes, chemicals, diseases and drugs. Its PATHWAY database supplies the manually drawn maps, and KEGG Mapper lets you place your own identifiers on them.
What are the four main metabolic pathways?
KEGG does not define a set of “four main” pathways. Its PATHWAY page lists Metabolism as one of seven categories, and the numbering scheme includes global (011xx) and overview (012xx) maps. Textbook groupings of metabolism vary, so cite the source you are following.
What is a protein pathway?
The phrase is informal. In KEGG terms, a pathway map is a wiring diagram of molecular interactions, reactions and relations; organism-specific maps replace KOs with that organism’s gene identifiers.
What is a Gene Ontology enrichment analysis?
It is a statistical test of whether a gene list is over-represented among genes annotated to particular GO terms. It is separate from KEGG pathway enrichment, which tests against KEGG maps; see the comparison above.
Sources
- KEGG PATHWAY: kegg.jp/kegg/pathway.html (read 2026-11-07)
- KEGG overview: kegg.jp/kegg/kegg1.html (page updated 2026-10-28; read 2026-11-07)
- KEGG legal: kegg.jp/kegg/legal.html (page dated 2024-10-01; read 2026-11-07)
- KEGG Mapper Search: kegg.jp/kegg/mapper/search.html (read 2026-11-07)
