Kyoto Encyclopedia of Genes and Genomes (KEGG)

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Encyclopedia of Genes, Genomes, and Pathways


Last updated: May 2009

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About Kyoto Encyclopedia of Genes and Genomes (KEGG)

Kyoto Encyclopedia of Genes and Genomes (KEGG) began primarily as a pathway database[1]. KEGG was described in the NAR database issue in 1999[2], 2000[3], 2002[4], 2004[5], and 2006[6]. As KEGG has grown, many new features have been incorporated, and KEGG is heavily cited by other papers.


KEGG is best known for their display of biochemical pathways, but many other functions are now available at KEGG. KEGG is a collection of about 20 databases, which can be divided into three groups covering different biological spaces:

  • Genes
    • KEGG Genes - manually curated from completely sequenced genomes
    • DGENES - draft genomes
    • EGENES - from EST contigs
    • KEGG Orthology - manually defined ortholog groups based on KEGG pathways and BRITE functional hierarchies
    • KEGG SSDB - Seq similarity scores
  • Chemicals and Ligands
    • Ligand
  • Systems
    • KEGG Pathway
    • KEGG Brite

Using Kyoto Encyclopedia of Genes and Genomes (KEGG)


Viewing pathways

KEGG allows highlighting of enzymes in a reference pathway that are present in a specific organism

Different pathways can be accessed from a menu on the KEGG pathway page. Each set of pathways is a manually drawn system diagram. Boxes show the EC number for each enzyme. Clicking on a shaded box links to a page for that enzyme from the highlighted organism. Pathways can also be shown as a reference pathway without highlighting. In this case, clicking on a box gives a summary with links to the activity in different organisms.


query by b# (
query by z# (
query by esc# (
query by c# (
query by stm# (
query by jw# (
Enzyme data: EC# mapped to b# (
Pathway data: pathway# and EC# mapped to b# (

Usage examples

Add links to additional pages describing success stories here.

Other sites with related content



Web Services/API

KEGG has both a WSDL/SOAP, and an XML description of KEGG metabolic maps using KGML, the KEGG Markup Language



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See Help:References for how to manage references in EcoliWiki.

  1. Ogata, H et al. () Computation with the KEGG pathway database. BioSystems 47 119-28 PubMed
  2. Ogata, H et al. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27 29-34 PubMed
  3. Kanehisa, M & Goto, S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28 27-30 PubMed
  4. Kanehisa, M et al. (2002) The KEGG databases at GenomeNet. Nucleic Acids Res. 30 42-6 PubMed
  5. Kanehisa, M et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 D277-80 PubMed
  6. Kanehisa, M et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34 D354-7 PubMed

External Links

Kyoto Encyclopedia of Genes and Genomes (KEGG)

Discussion of Kyoto Encyclopedia of Genes and Genomes (KEGG) on other websites