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Cited by 5,833Bioinformatics and Genomic NetworksGenomics and Phylogenetic StudiesMicrobial Metabolic Engineering and Bioproduction

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KEGG for taxonomy-based analysis of pathways and genomes

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Kanehisa, Minoru, Furumichi, Miho, Sato, Yoko, Kawashima, Masayuki, Ishiguro-Watanabe, Mari·2023·Nucleic Acids Research
DOI 10.1093/nar/gkac963PMC PMC9825424
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Abstract

KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.

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Figure 1. KEGG is an integrated database containing various biological objects (contents) stored in sixteen databases in four categories. Each object (database entry) is identified by the KEGG identifier (kid) as defined here. Except for GENES and a few other databases, the KEGG identifier takes the form of a prefix followed by a five-digit number. Manually created reference pathway maps, reference Brite hierarchies and reference modules are computationally expanded to organism-specific ones by converting KO identifiers (K numbers) to GENES identifiers in individual organisms (see text).
Figure 1. KEGG is an integrated database containing various biological objects (contents) stored in sixteen databases in four categories. Each object (database entry) is identified by the KEGG identifier (kid) as defined here. Except for GENES and a few other databases, the KEGG identifier takes the form of a prefix followed by a five-digit number. Manually created reference pathway maps, reference Brite hierarchies and reference modules are computationally expanded to organism-specific ones by converting KO identifiers (K numbers) to GENES identifiers in individual organisms (see text).CC BY-NC · PubMed Central
Figure 2. Simple URLs, called KEGG weblinks, to retrieve and analyze KEGG objects (database entries). The entry operation retrieves any object specified by the KEGG identifier in the flat-file format. The pathway, brite, module or network operation retrieves a molecular network object specified by the KEGG identifier with optional highlighting of network nodes given in the argument. The genome operation retrieves the genome map of a given organism with optional specification of a gene location. The pathway, brite and genome operations actually launch specialized tools enabling further analysis. In the URL form, www.kegg.jp may be replaced by www.genome.jp for accessing the GenomeNet mirror site.
Figure 2. Simple URLs, called KEGG weblinks, to retrieve and analyze KEGG objects (database entries). The entry operation retrieves any object specified by the KEGG identifier in the flat-file format. The pathway, brite, module or network operation retrieves a molecular network object specified by the KEGG identifier with optional highlighting of network nodes given in the argument. The genome operation retrieves the genome map of a given organism with optional specification of a gene location. The pathway, brite and genome operations actually launch specialized tools enabling further analysis. In the URL form, www.kegg.jp may be replaced by www.genome.jp for accessing the GenomeNet mirror site.CC BY-NC · PubMed Central
Figure 3. The KEGG taxonomy browser, implemented as the Brite hierarchy viewer for taxonomy files, is now linked from the Organism menu of each KEGG pathway map. This example is linked from the lysine biosynthesis pathway map00300, included here by highlighting the plant-specific module M00527, and provides a taxonomy-based global view of organisms and organism groups in which the pathway and associated modules are present.
Figure 3. The KEGG taxonomy browser, implemented as the Brite hierarchy viewer for taxonomy files, is now linked from the Organism menu of each KEGG pathway map. This example is linked from the lysine biosynthesis pathway map00300, included here by highlighting the plant-specific module M00527, and provides a taxonomy-based global view of organisms and organism groups in which the pathway and associated modules are present.CC BY-NC · PubMed Central
Figure 4. The KEGG genome browser is used to display syntenic regions in multiple genomes. Here, a region of eight genes represented as a sequence of eight K numbers is searched against all KEGG organisms. The result of matching organisms is shown in the taxonomy tree, from which selected genomes are displayed by aligning syntenic regions. Color coding is based on the functional category in KEGG.
Figure 4. The KEGG genome browser is used to display syntenic regions in multiple genomes. Here, a region of eight genes represented as a sequence of eight K numbers is searched against all KEGG organisms. The result of matching organisms is shown in the taxonomy tree, from which selected genomes are displayed by aligning syntenic regions. Color coding is based on the functional category in KEGG.CC BY-NC · PubMed Central

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Metadata

Authors
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M., & Ishiguro-Watanabe, M.
Affiliations
  • Kyoto University (JP)
  • Fujitsu (Japan) (JP)
  • Network Support Co. Ltd., Hakata-ku , Fukuoka 812-0011, Japan
  • Institute of Medical Science, The University of Tokyo (JP)
Corresponding author
Kanehisa, Minoru
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2022-10-27
Volume
51
Issue
D1
Pages
D587-D592
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkac963
PMC
PMC9825424
OpenAlex
W4307425304
Cited by
5,833
References
12
Citations by year
2026: 911 · 2025: 1421 · 2024: 1899 · 2023: 1560 · 2022: 39
FWCI
461.30
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Institutional Repositories DataBase (IRDB) (submittedVersion)
  • Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by-nc)
Funders
Japan Science and Technology Agency
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords
KEGG, pathway maps, genome annotation, KEGG Orthology, eukaryotic genomes, viruses, genome browser
MeSH terms
Databases, Factual, Genome, Genomics, Databases, Genetic

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