May 1998

A Quick Guide to KEGG:

Kyoto Encyclopedia of Genes and Genomes
http://www.genome.ad.jp/kegg/

1. Background
Objectives of the KEGG Project
1. Computerize current knowledge of molecular and cellular biology in terms of
the pathway of interacting molecules or genes (PATHWAY database)
2. Maintain gene catalogs of all sequenced organisms and link each gene product
to a pathway component (GENES database)
3. Organize a database of all chemical compounds in living cells and link each
compound to a pathway component (LIGAND database)
4. Develop new bioinformatics technologies for functional genomics, such as
pathway comparison, pathway reconstruction, and pathway design
See also: Kanehisa, M., "A database for post-genome analysis", Trends Genet. 13, 375-376 (1997).
Kanehisa, M., "Linking databases and organisms: GenomeNet resources in Japan",
Trends Biochem. Sci. 22, 442-444 (1997).

Data Representation in KEGG

Entity
Binary relation
Network
Genome
Neighbor
Hierarchy
Pathway

- a molecule or a gene
- a relation between two entities
- a graph formed from a set of related entities
- physical closeness of genes
- similarity of molecules or genes; e.g., sequence similarity
- hierarchical classification of molecules or genes
- biochemical pathway or genetic pathway

Entities

Genomes

Binary Relations

Neighbor
Networks

Hierarchy

Pathway

2. Initiating KEGG queries

Search and Prediction Tools

Search pathway maps by:
EC numbers
Compound numbers
Gene names
Sequence similarity

Pathway Map
Browser

Ortholog Group
Table Browser

Search ortholog tables by:

Sequence similarity
Genome Map
Browser (Java)
for complete
genomes

Search genome maps by:

Gene names
Search two genome maps for:
Homologous gene clusters

Catalog
(Hierarchical
Text) Browser

Other Search Tools

Hierarchical Text Search
DBGET/LinkDB Search

25 species
including
13 complete
genomes

Genome Map Comparison Tool

(to be available soon)

Human Genome
Map Browser

DBGET Database Links

KEGG
Genes

Pathway

LinkDB
LIGAND

BRITE
DBGET

OMIM

DBGET/LinkDB is the integrated

database retrieval system that forms
the basis of the Japanese GenomeNet
service (http://www.genome.ad.jp/).

AAindex

PRF

Medline

GenBank
DNA

Protein

LITDB

EMBL

SwissProt

EPD

TRANSFAC

PIR

PROSITE

PMD

PDB

PDBSTR

3. Correlation of a physical unit and a functional unit of genes

Select a specific area

of a genome map
Click this button to examine
the biochemical pathway
formed by the gene products

A set of sequences that may or may not be

located closely in the genome can be
entetered in this search box to see if a
pathway can properly be formed. This is
done by sequence similarity search against
a reference organism.

4. Gene function assignment by reconstruction of functional units

The knowledge of functional units in molecular

pathways and assemblies is best represented in
KEGG by the ortholog/paralog group tables
such as shown here. When a functional unit is
completely reconstructed from a set of genes,
this confirms the correctness of individual gene
function assitgnments. Furthermore, the search
against the KEGG tables often provides a more
detailed picture of predicted function, such as
the substrate specificity of ABC transporters.

5. Ab initio reconstruction of pathways

The reconstruction above is a
homology modeling based on
comparison against the reference
pathways. In contrast, ab initio
reconstruction requires no
references but a set of binary
realtions that is used to generate
possible pathways. The tool shown
left will generate all possible
chemical reaction pathways between
two compounds from a given set of
substrate-product binary relations.
AB
BC
CD
BE
E' F

G
E

ABCD
E'

EF