KEGG数据库介绍

genechip

KEGG Overview1. KEGG DatabasesKEGG is an integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information as shown below. Genomic and chemical information represents the molecular building blocks of life in the genomic and chemical spaces, respectively, and systems information represents functional aspects of the biological systems, such as the cell and the organism, that are built from the building blocks. KEGG has been widely used as a reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

Category	Database	Content
Systems information	KEGG PATHWAY	Pathway maps for metabolism and other cellular processes, as well as human diseases; manually created from published materials
	KEGG BRITE	Functional hierarchies (ontologies) representing our knowledge on various aspects of biological systems; manually created from published materials
	KEGG MODULE	Tighter functional units for pathways and complexes; manually defined
	KEGG DISEASE	List of disease genes and molecules; manually entered from published materials
	KEGG DRUG	Chemical structures and associated information of approved drugs in Japan, USA, and Europe; manually entered from published materials
	KEGG EDRUG	Chemical components and associated information of crude drugs and other natural products; manually entered from published materials
Genomic information	KEGG ORTHOLOGY	KEGG Orthology (KO) groups based on PATHWAY and BRITE; manually defined
	KEGG GENOME	Genome maps and organism information; generated from RefSeq and other public resources
	KEGG GENES	Gene catalogs of complete genomes with manual annotation; generated from RefSeq and other public resources
	KEGG SSDB	Sequence similarity scores and best-hit relations; computationally derived from GENES by pairwise genome comparisons of all protein-coding genes
	KEGG DGENES	Gene catalogs of draft genomes with automatic annotation; generated from web resources
	KEGG EGENES	Gene catalogs (consensus contigs) of EST data with automatic annotation; generated from dbEST
	KEGG MGENES	Gene catalogs of metagenomes with automatic annotation; generated from NCBI resources
Chemical information	KEGG COMPOUND	Chemical compounds; manually entered from published materials[/td]
	KEGG GLYCAN	Glycans; manually entered from published materials
	KEGG REACTION	Chemical reactions; manually defined from ENZYME and PATHWAY
	KEGG RPAIR	Chemical structure transformation patterns; manually defined from REACTION
	KEGG RCLASS	Reaction class defined by chmeical structure transformation patterns of main reactant pairs; generated from RPAIR with annotation
	KEGG ENZYME	Enzyme nomenclature; generated from ExplorEnz with annotation by KEGG

2. KEGG ObjectsKEGG is a computer representation of the biological systems. It is based on the concept of graph for representation and manipulation of various KEGG objects from molecular to higher levels. Mathematically, a graph is a set of nodes (KEGG objects) and edges (biological relationships). Each of the KEGG objects (database entries) is given an unique identifier shown below.

Release	Database	Object Identifier
1995	KEGG PATHWAY	map number
	KEGG GENES	locus_tag / GeneID
	KEGG ENZYME	EC number
	KEGG COMPOUND	C number
2000	KEGG GENOME	organism code / T number
2001	KEGG REACTION	R number
2002	KEGG ORTHOLOGY	K number
2003	KEGG GLYCAN	G number
2004	KEGG RPAIR	RP number
2005	KEGG BRITE	br number
	KEGG DRUG	D number
2007	KEGG MODULE	M number
2008	KEGG DISEASE	H number
2010	KEGG EDRUG	E number
	KEGG RCLASS	RC number

KEGG objects are linked to/from major life science databases. KEGG objects are also part of the Web; they can be found by Web search engines.

Graph	Node	Edge	Search and Analysis
KEGG	KEGG object	Biological relationship	KEGG
Integrated database	Entry	Cross-reference link	DBGET, Entrez, SRS, etc.
Web	Web page	Hyperlink	Google, etc.

3. Network HierarchyThe molecular interaction/reaction network is the most unique data object in KEGG, which is stored as a collection of pathway maps (graphical diagrams) in the PATHWAY database. Reflecting the map resolution, KEGG PATHWAY is organized in a hierarchy. The top two levels in the current hierarchy is the following.

First Level	Second Level
Metabolism	Carbohydrate Metabolism Energy Metabolism Lipid Metabolism Nucleotide Metabolism Amino Acid Metabolism Metabolism of Other Amino Acids Glycan Biosynthesis and Metabolism Metabolism of Cofactors and Vitamins Metabolism of Terpenoids and Polyketides Biosynthesis of Other Secondary Metabolites Xenobiotics Biodegradation and Metabolism
Genetic Information Processing	Transcription Translation Folding, Sorting and Degradation Replication and Repair
Environmental Information Processing	Membrane Transport Signal Transduction Signaling Molecules and Interaction
Cellular Processes	Transport and Catabolism Cell Motility Cell Growth and Death Cell Communication[/td]
Organismal Systems	Immune System Endocrine System Circulatory System Digestive System ExcretorySystem Nervous System Sensory System Development Environmental Adaptation
Human Diseases	Cancers Immune System Diseases Neurodegenerative Diseases Cardiovascular Diseases Metabolic Diseases Infectious Diseases

4. Network ReconstructionOriginally, the integration of pathway information and genomic information was first achieved in KEGG by the EC numbers. Once the EC numbers were correctly assigned to enzyme genes in the genome, organism-specific pathways could be generated automatically by matching against the networks of EC numbers (enzymes) in the reference metabolic pathways. However, in order to incorporate non-metabolic pathways and to overcome various problems inherent in the enzyme nomenclature, a new scheme based on the ortholog IDs was introduced replacing the EC numbers. KO (KEGG Orthology) is a further extension of ortholog IDs based on not only the pathway maps but also the BRITE functional hierarchies, most notably classifications of protein families.

Period	Identifier	Mapping	Assignment
1995-1999	EC number	Metabolic pathways	Domain based[/td]
2000-2002	Ortholog ID	Metabolic and regulatory pathways	Domain based[/td]
2003-	KO	Pathways and BRITE hierarchies	Gene based

Thus, under the current KO system, the KO identifiers (K numbers) are placed at the fourth (lowest) level in the network hierarchy shown above, or at the lowest level of the BRITE hierarchy.
5. BRITE Functional HierarchyThe BRITE database is a collection of hierarchical text files and binary relation files. It is intended to supplement the PATHWAY database in two ways. One is to computerize higher-level knowledge that cannot easily be represented as molecular interaction/reaction networks, in terms of the hierarchically structured vocabulary. The other is to integrate our knowledge about the genomic space (K numbers) with different types of knowledge in the chemical space (C/D/G/R/RP/EC numbers in the LIGAND database). The BRITE collection is currently categorized as follows.

Top Category	Second Category
Genes and Proteins	Network hierarchy Protein families
Compounds and Reactions	Compounds Reactions Compoound interactions
Drugs and Diseases	Drugs Diseases
Cells and Organisms	Organisms

References

• Kanehisa, M.; Toward pathway engineering: a new database of genetic and molecular pathways. Science & Technology Japan, No. 59, pp. 34-38 (1996). [pdf]
• Kanehisa, M.; A database for post-genome analysis. Trends Genet. 13, 375-376 (1997). [pubmed]
• Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 27, 29-34 (1999). [pubmed] [pdf]
• Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000). [pubmed] [pdf]
• Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.; The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002). [pubmed] [pdf]
• Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., and Hattori, M.; The KEGG resources for deciphering the genome. Nucleic Acids Res. 32, D277-D280 (2004). [pubmed] [pdf]
• Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006). [pubmed] [pdf]
• Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., and Yamanishi, Y.; KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008). [pubmed] [pdf]
• Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010). [pubmed] [pdf]
  

Last updated: January 1, 2011