KEGG for linking genomes to life and the environment

By Minoru Kanehisa, M. Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, T. Tokimatsu and 1 more. Nucleic Acids Res., 2007

6,544 citations recorded by the source corpus.

KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.

Subfields: Molecular Biology

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Citations in the corpus

Genome-scale models of bacterial metabolism: reconstruction and applications (2008, background): “Three main resources provide this type of information: MetaCyc (Caspi et al ., 2006), KEGG Modules (Kanehisa et al ., 2007), and SEED (Overbeek et al ., 2005) (see Tables 1 and 2).”
KEGG for integration and interpretation of large-scale molecular data sets (2011, methodology): “KEGG MODULE was originally introduced to define tighter functional units than KEGG PATHWAY (6) so that the pathway information in KEGG would be represented in three resolutions: global maps (for metabolism), regular maps and modules.”
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates (2012, background): “, 2008), and Kyoto Encyclopedia of Genes and Genomes (KEGG) modules and pathways (Kanehisa et al., 2008).”
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework (2010, methodology): “Amino acid sequences of proteins coded in the human genome were obtained from the KEGG GENES database (Kanehisa et al., 2008).”
The Universal Protein Resource (UniProt) in 2010 (2009, methodology): “The chemical perspective is based on KEGG LIGAND compounds and reactions with the kind permission of the Kanehisa Laboratory (16).”
KEGG Atlas mapping for global analysis of metabolic pathways (2008, methodology): “jp/kegg/) (1) has been developed to represent such knowledge in terms of the molecular interaction and reaction networks and has enabled ‘pathway mapping’, which is to map large-scale data sets to the KEGG reference pathways for understanding higher-level functional meanings.”
The NCBI BioSystems database (2009, methodology): “Fortunately, a considerable number of resources have been created to address this issue: the Pathguide (1) resource lists nearly 300 pathway resources alone, including KEGG (2), Reactome (3), PID (4), PharmGKB (5), GenMAPP (6), Biocyc (7) and many others.”
GeNGe: systematic generation of gene regulatory networks (2009, neutral): “A model can be constructed from various databases, such as KEGG (Kanehisa et al., 2008), Reactome (Matthews et al.”
Reactome knowledgebase of human biological pathways and processes (2008, neutral): “html) (4) and MetaCyc (http://metacyc.”
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling (2010, background): “Regarding the gene modules that can be used in order to produce a functional interpretation of the results, many possibilities are available, including functional definitions [GO (2), GOSlim, KEGG (3), Biocarta (http://www .”