Skip to content
DraconiticResearch
Search Sources API
197,787 studies31 sourcesUpdated 3 min ago
Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

KEGG for characterizing genomes and pathways in the biosphere

  • Minoru Kanehisa1
  • Miho Furumichi1
  • Yoko Sato2
  • Yuriko Matsuura2
  • Mari Ishiguro-Watanabe3
  1. 1Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011 ,
  2. 2Pathway Solutions Inc., 2-16-3 Higashi-Shinbashi , Minato-ku, Tokyo 105-0021 ,
  3. 3Human Genome Center, Institute of Medical Science, University of Tokyo , Minato-ku, Tokyo 108-8639 ,
Open at sourcePDFDOICite

Abstract

The KEGG database (https://www.kegg.jp) has been developed as a model of the biological systems. By organizing knowledge of cellular and organism-level functions in the form of molecular wiring diagrams, the model enables generating new knowledge and finding practical applications. The KO (KEGG Orthology) dataset plays the basic role of organizing knowledge. KO is an ortholog with functional relevance, generalizing experimental evidence in specific organisms to other organisms. KEGG molecular networks, including pathway maps and modules, are generic networks with KOs as network nodes, and thus KEGG mapping from genomes to pathways can be applied to any organism. As the number of KOs increases and the KO annotation rate improves, KEGG mapping is further expanded. A set of KOs in the genome and a set of modules in the metabolic pathways are now used to characterize various data objects in the biosphere, including organisms, organism groups, microbiomes, viruses, and their combinations, such as endosymbiont–host, microbiome–host, and virus–host relationships. Furthermore, a simple measure of similarity either by KO compositions or module compositions is introduced to compare organism groups. The resulting similarity dendrograms possibly reflect similarity of cellular functions or, more specifically, metabolic functions, which can be compared with phylogenetic trees.

Related

  1. KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires
    Minoru Kanehisa, Yoko Sato
    Protein SciencePeer-reviewedCC BY-NC7 citedMolecular biology & gene regulationOpenAlex
  2. Gene body architecture predicts isoform diversity across eukaryotic genomes
    Quinton Brohart, Arvind Mer
    BMC GenomicsPeer-reviewedCC BY-NC-ND 4.0Molecular biology & gene regulationCrossref
  3. Preface to the special issue “Cytoplasmic Genome Regulation: Genomes and Regulatory Mechanisms of Chloroplasts and Mitochondria”
    Tomohiko Kazama, Keiji Numata, Shin-ichi Arimura
    Plant BiotechnologyPeer-reviewedCC BYFull textMolecular biology & gene regulationJ-STAGE
  4. Characterization and comparative analysis of the complete mitochondrial genomes of two Amorphophallus species (Araceae)
    Haoliang Shi, Min Yang, Ying Qi +8
    BMC GenomicsPeer-reviewedCC BY-NC-ND 4.0Molecular biology & gene regulationCrossref
  5. Comparative mitogenomics of two parasitic isopods, Ione cornuta and Pseudione longicauda, with putatively linear mitochondrial genomes
    Xiaowan Ma, Luoyang Chen, Teng Huang +7
    BMC GenomicsPeer-reviewedCC BY-NC-ND 4.0Molecular biology & gene regulationCrossref

Cite

BibTeXRIS
BibTeX
@article{kanehisa2026kegg,
  title = {{KEGG for characterizing genomes and pathways in the biosphere}},
  author = {Minoru Kanehisa and Miho Furumichi and Yoko Sato and Yuriko Matsuura and Mari Ishiguro-Watanabe},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1042},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1042/9002504},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - KEGG for characterizing genomes and pathways in the biosphere
AU  - Minoru Kanehisa
AU  - Miho Furumichi
AU  - Yoko Sato
AU  - Yuriko Matsuura
AU  - Mari Ishiguro-Watanabe
PY  - 2026
DA  - 2026/10/27
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1042
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1042/9002504
AB  - The KEGG database (https://www.kegg.jp) has been developed as a model of the biological systems. By organizing knowledge of cellular and organism-level functions in the form of molecular wiring diagrams, the model enables generating new knowledge and finding practical applications. The KO (KEGG Orthology) dataset plays the basic role of organizing knowledge. KO is an ortholog with functional relevance, generalizing experimental evidence in specific organisms to other organisms. KEGG molecular networks, including pathway maps and modules, are generic networks with KOs as network nodes, and thus KEGG mapping from genomes to pathways can be applied to any organism. As the number of KOs increases and the KO annotation rate improves, KEGG mapping is further expanded. A set of KOs in the genome and a set of modules in the metabolic pathways are now used to characterize various data objects in the biosphere, including organisms, organism groups, microbiomes, viruses, and their combinations, such as endosymbiont–host, microbiome–host, and virus–host relationships. Furthermore, a simple measure of similarity either by KO compositions or module compositions is introduced to compare organism groups. The resulting similarity dendrograms possibly reflect similarity of cellular functions or, more specifically, metabolic functions, which can be compared with phylogenetic trees.
SN  - 0305-1048
SN  - 1362-4962
ER  -