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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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: Kanehisa, Minoru
Sato, Yoko
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: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor)
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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