Using the KEGG Database Resource

Mao Tanabe1, Minoru Kanehisa1

1 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.12
DOI:  10.1002/0471250953.bi0112s38
Online Posting Date:  June, 2012
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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

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Table of Contents

  • Introduction
  • Basic Protocol 1: The KEGG Database Resource: Getting Started
  • Basic Protocol 2: KEGG Pathway: Metabolic Pathway Map
  • Basic Protocol 3: KEGG Pathway: Genome Comparison and Combination
  • Basic Protocol 4: KEGG Pathway: Regulatory Pathway Map
  • Basic Protocol 5: KEGG Pathway: Disease Pathway Map
  • Basic Protocol 6: KEGG Drug: Network‐Based Drug Information Resource
  • Basic Protocol 7: KEGG Disease: Disease Genes and Pathogen Genomes
  • Basic Protocol 8: KEGG Disease/Drug Mapping
  • Basic Protocol 9: KEGG BRITE: Functional Hierarchy of Genes and Proteins
  • Basic Protocol 10: KEGG BRITE: Functional Hierarchy of Other Entities
  • Basic Protocol 11: KEGG GENES: Gene Catalogs of Complete Genomes
  • Basic Protocol 12: KEGG SSDB: Analysis of Gene/Protein Universe
  • Basic Protocol 13: KEGG Orthology: Linking Genome to Molecular Network
  • Basic Protocol 14: KEGG GENOME: Genome Metadata and Taxonomy
  • Basic Protocol 15: KEGG LIGAND: Chemical Structure and Similarity Search
  • Basic Protocol 16: KEGG LIGAND: Biochemical Reaction and Path Prediction
  • Basic Protocol 17: KEGG MODULE: Functional Units and Signatures
  • Basic Protocol 18: KEGG Mapper: Pathway Mapping
  • Basic Protocol 19: KEGG Mapper: BRITE Mapping
  • Basic Protocol 20: KEGG Atlas: Advanced Visualization Tool
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
   Aoki, K.F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S., and Kanehisa, M. 2004. KCaM (KEGG Carbohydrate Matcher): A software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. 32:W267‐W272.
   Goto, S., Okuno, Y., Hattori, M., Nishioka, T., and Kanehisa, M. 2002. LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30:402‐404.
   Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M. 2003. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 125:11853‐11865.
   Hattori, M., Tanaka, N., Kanehisa, M., and Goto, S. 2010. SIMCOMP/SUBCOMP: Chemical structure search servers for network analyses. Nucleic Acids Res. 38:W652‐W656.
   Kanehisa, M. 1997. A database for post‐genome analysis. Trends Genet. 13:375‐376.
   Kanehisa, M. and Goto, S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28:27‐30.
   Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:42‐46.
   Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:D277‐D280.
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   Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M. 2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38:D355‐D360.
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   Kotera, M., Okuno, Y., Hattori, M., Goto, S., and Kanehisa, M. 2004. Computational assignment of the EC numbers for genomic‐scale analysis of enzymatic reactions. J. Am. Chem. Soc. 126:16487‐16498.
   McDonald, A.G., Boyce, S., and Tipton, K.F. 2009. ExplorEnz: The primary source of the IUBMB enzyme list. Nucleic Acids Res. 37:D593‐D597.
   Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., and Kanehisa, M. 2007. KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35:W182‐W185.
   Moriya, Y., Shigemizu, D., Hattori, M., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M. 2010. PathPred: An enzyme‐catalyzed metabolic pathway prediction server. Nucleic Acids Res. 38:W138‐W143.
   Pruitt, K.D., Tatusova, T., Brown, G.R., and Maglott, D.R. 2012. NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res. 40:D130‐D135.
   Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., and Kanehisa, M. 2011. Network‐based analysis and characterization of adverse drug‐drug interactions. J. Chem. Inf. Model. 51:2977‐2985.
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