KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires
- 1Institute for Chemical Research Kyoto University Uji, Kyoto Japan
- 2Pathway Solutions Inc. Minato‐ku, Tokyo Japan
Abstract
The KEGG Orthology (KO) system has been used as a basic framework of the KEGG database for linking genes in the genome to pathways and other molecular networks. KOs are manually defined orthologs representing conserved genes with relevance to molecular and higher-level functions. Here, the KO system is used to define genomic features, including the gene content by the composition of KOs and the gene order on the chromosome by the sequence of KOs, and to compare organisms, organism groups and viruses according to the similarity of KO compositions and KO sequences. The compositions of KEGG modules, manually defined functional sets of KOs, and VOGs, computationally derived ortholog groups for viruses, are also used as genomic features. The similarity analysis of organism groups by KO compositions has revealed a close relationship of Bacteria and Archaea, which differs from the three domains of life in evolution, but which is likely to reflect similarity of metabolic and other cellular functions represented by KOs. A collection of tools is named KEGG Syntax (https://www.kegg.jp/kegg/syntax/) and can be used to analyze the user's data as well as the genomes already registered in KEGG.
Related
- The brilliant future of non-traditional model organisms in biology
- dictyBase 2026: a reimplementation of the Dictyostelium model organism database on minimal infrastructure
- Molecular Science of Eicosapentaenoic Acid (EPA) Omega-3 Fatty Acid Using Nannochloropsis oceanica as a Model Organism
- Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites
- Using Bayesian inference to characterize cell-size regulation across organisms
BibTeX
@article{kanehisa2026kegg,
title = {{KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires}},
author = {Minoru Kanehisa and Yoko Sato},
journal = {Protein Science},
year = {2026},
month = may,
doi = {10.1002/pro.70652},
url = {https://doi.org/10.1002/pro.70652},
note = {CC BY-NC},
}
RIS
TY - JOUR
TI - KEGG Syntax for comparison of organisms, organism groups, and viruses by conserved gene repertoires
AU - Minoru Kanehisa
AU - Yoko Sato
PY - 2026
DA - 2026/05/21
JO - Protein Science
DO - 10.1002/pro.70652
UR - https://doi.org/10.1002/pro.70652
AB - The KEGG Orthology (KO) system has been used as a basic framework of the KEGG database for linking genes in the genome to pathways and other molecular networks. KOs are manually defined orthologs representing conserved genes with relevance to molecular and higher-level functions. Here, the KO system is used to define genomic features, including the gene content by the composition of KOs and the gene order on the chromosome by the sequence of KOs, and to compare organisms, organism groups and viruses according to the similarity of KO compositions and KO sequences. The compositions of KEGG modules, manually defined functional sets of KOs, and VOGs, computationally derived ortholog groups for viruses, are also used as genomic features. The similarity analysis of organism groups by KO compositions has revealed a close relationship of Bacteria and Archaea, which differs from the three domains of life in evolution, but which is likely to reflect similarity of metabolic and other cellular functions represented by KOs. A collection of tools is named KEGG Syntax (https://www.kegg.jp/kegg/syntax/) and can be used to analyze the user's data as well as the genomes already registered in KEGG.
SN - 0961-8368
SN - 1469-896X
ER -