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December 12, 2007Nucleic Acids Research7,109 citationsOpen Access

KEGG for linking genomes to life and the environment

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MKMinoru KanehisaMAMichihiro ArakiSGSusumu Goto

Key Points

  • To present expansions to the KEGG database for integrating genomic, transcriptomic, and chemical data to infer cellular, organismal, and environmental systems.
  • Applied KEGG PATHWAY mapping to align genomic and transcriptomic sequences against reference molecular interaction networks.
  • Utilized KEGG BRITE ontologies to systematically organize functional hierarchies of molecules, cells, organisms, diseases, and drugs.
  • Curated clinical and pharmacological databases, compiling all approved therapeutics in the United States and Japan into KEGG DRUG and linking disease mechanisms in KEGG DISEASE.
  • Supplemented KEGG PATHWAY with a comprehensive global metabolic map consolidating approximately 120 individual metabolic pathway maps.
  • Introduced KEGG MODULE to catalog smaller conserved functional units and molecular complexes for modular network reconstruction.
  • Expanded translational utility by integrating disease genes, molecular pathways, approved therapeutics, and diagnostic biomarkers across KEGG DRUG and KEGG DISEASE.

Abstract

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.

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Cite This Study

Kanehisa et al. (2007) studied this question.

synapsesocial.com/papers/69d71bd7ef370a38abf5092fhttps://doi.org/10.1093/nar/gkm882
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