KEGG for taxonomy-based analysis of pathways and genomes

KEGG for taxonomy-based analysis of pathways and genomes

2023, Vol. 51, Database issue | Minoru Kanehisa, Miho Furumichi, Yoko Sato, Masayuki Kawashima and Mari Ishiguro-Watanabe
The KEGG database is a manually curated resource that integrates various biological objects, including systems, genomic, chemical, and health information. Each object is identified by a KEGG identifier (kid), which can be used to retrieve specific data through URLs. The KEGG pathway map viewer, Brite hierarchy viewer, and KEGG genome browser are specialized tools that can be launched by appending specific URLs. The database has expanded to include a growing number of eukaryotic genomes, enhancing its representation of organisms in the taxonomic tree. Taxonomy files are generated for classification, and the Brite hierarchy viewer facilitates taxonomy mapping, enabling the analysis of conserved functional and physical links among genes across different organism groups. The KEGG Orthology (KO) system, which assigns K numbers to genes, allows for the expansion of reference pathway maps into organism-specific maps. The database also includes datasets for genes, genomes, and viruses, with detailed taxonomic classification and functional annotations. The KEGG Genome Browser is a new tool for analyzing chromosomal locations of genes, particularly for identifying conserved gene orders and synteny among KEGG organisms. Future plans include extending the NETWORK database to focus on viral perturbations. KEGG is supported by community funding and is updated daily, with major updates announced every three months.The KEGG database is a manually curated resource that integrates various biological objects, including systems, genomic, chemical, and health information. Each object is identified by a KEGG identifier (kid), which can be used to retrieve specific data through URLs. The KEGG pathway map viewer, Brite hierarchy viewer, and KEGG genome browser are specialized tools that can be launched by appending specific URLs. The database has expanded to include a growing number of eukaryotic genomes, enhancing its representation of organisms in the taxonomic tree. Taxonomy files are generated for classification, and the Brite hierarchy viewer facilitates taxonomy mapping, enabling the analysis of conserved functional and physical links among genes across different organism groups. The KEGG Orthology (KO) system, which assigns K numbers to genes, allows for the expansion of reference pathway maps into organism-specific maps. The database also includes datasets for genes, genomes, and viruses, with detailed taxonomic classification and functional annotations. The KEGG Genome Browser is a new tool for analyzing chromosomal locations of genes, particularly for identifying conserved gene orders and synteny among KEGG organisms. Future plans include extending the NETWORK database to focus on viral perturbations. KEGG is supported by community funding and is updated daily, with major updates announced every three months.
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