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Using KEGG in the Transition from Genomics to Chemical Genomics

  • Kiyoko F. Aoki-KinoshitaEmail author
  • Minoru Kanehisa

Abstract

KEGG is well known as a useful pathway reference database, containing all of the major metabolic and signaling pathways such as carbohydrate, energy, lipid and amino acid metabolism, membrane transport and signal transduction. The latest addition to KEGG, the KEGG BRITE database, is a resource of hierarchical classifications of biological data, including pathway-based gene ortholog information, which, as a result, provides genetic information, computed in the biological context within which genes are expressed. Moreover, BRITE contains chemical compound data derived from the KEGG COMPOUND database, which has been classified based on compound structure similarity such that they may be analyzed as ligands via hierarchical classifications. Thus, KEGG provides a valuable resource for genomic analysis in terms of its wealth of data in the PATHWAY, GENES and ENZYME knowledgebases, while at the same time providing a unique but important resource for understanding the chemical environment in which these biological processes occur. The concept of chemical compound similarity is increasingly being utilized in the latest research of ligand prediction and drug design. Such research will be able to make use of the data in KEGG BRITE as well as the new KEGG DRUG database containing maps of drug development and drug classifications. In this chapter, we will provide an introduction to the KEGG databases as well as the latest research in chemical genomics using KEGG. We will also describe some of the available practical means of accessing KEGG, such as directly via a computer program using the KEGG API.

Keywords

KEGG Pathways Orthologs Chemical genomics 

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Department of Bioinformatics, Faculty of EngineeringSoka University, 1-236 Tangi-machiHachiojiJapan
  2. 2.Kyoto UniversityGokashoJapan

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