Unit

UNIT 1.12 Using the KEGG Database Resource

  1. Mao Tanabe,
  2. Minoru Kanehisa

Published Online: 1 JUN 2012

DOI: 10.1002/0471250953.bi0112s38

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Tanabe, M. and Kanehisa, M. 2012. Using the KEGG Database Resource. Current Protocols in Bioinformatics. 38:1.12.1–1.12.43.

Author Information

  1. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan

Publication History

  1. Published Online: 1 JUN 2012

Abstract

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of cells and organisms from both high-level and genomic perspectives. It is a self-sufficient, integrated resource consisting of genomic, chemical, and network information, with cross-references to numerous outside databases. The genomic and chemical information is a complete set of building blocks (genes and molecules) and the network information includes molecular wiring diagrams (interaction/reaction networks) and hierarchical classifications (relation networks) to represent high-level functions. This unit describes protocols for using KEGG, focusing on molecular network information in KEGG PATHWAY, KEGG BRITE, and KEGG MODULE, perturbed molecular networks in KEGG DISEASE and KEGG DRUG, molecular building block information in KEGG GENES and KEGG LIGAND, and a mechanism for linking genomes to molecular networks in KEGG ORTHOLOGY (KO). All of these many protocols enable the user to take advantage of the full breadth of the functionality provided by KEGG. Curr. Protoc. Bioinform. 38:1.12.1-1.12.43. © 2012 by John Wiley & Sons, Inc.

Keywords:

  • KEGG pathway map;
  • BRITE functional hierarchy;
  • molecular network;
  • genome annotation;
  • chemical information analysis