Databases and Systems

can be used for gene function assignments. The KEGG ortholog group tables are a
clean reference data set of orthologous relations that is intended to make this process
easier. The table contains not only the information of orthologous and paralogous
genes, but also the information of the group of genes that is supposed to form a
functional unit, such as a regulatory unit in the metabolic pathway or a molecular unit
of assembly. Thus, the ortholog group tables represent a library of 'network motifs' or
conserved local network patterns that are related to functional meanings. They are
maintained manually with the aid of network comparison tools in KEGG.
Molecular catalogs
The molecular catalogs are to be used for representing functional and structural
classifications of proteins, RNAs, other biological macromolecules, small chemical
compounds, and their assemblies. However, the current version of KEGG contains
only several tables, mostly for enzyme classifications.
Chemical compounds
The living cell contains a number of non-genetic compounds that are synthesized,
transported from outside, or simply carried over cell divisions. In order to represent a
complete network of molecular interactions, it is necessary to have a complete
catalog of compounds in the cell and possibly in the environment as well. The
COMPOUND section of the LIGAND database currently consists of over 5,000
chemical compounds, mostly metabolites with links to the location on the metabolic
pathways and to the enzymatic reactions involved. The COMPOUND entry also
contains the chemical structure that is entered manually using the ISIS system, and
the CAS number.
Enzymatic reactions
The information of enzymatic reactions and enzyme molecules is currently stored in
the ENZYME section of the LIGAND database. Work is in progress, however, to
organize the third REACTION section of the LIGAND database containing both
enzymatic and non-enzymatic reactions. A reaction between multi-substrates and
multi-products is decomposed into a set of binary relations or approximated by a
reaction between two major compounds. The reaction data are especially important
for computing possible chemical networks, from which possible gene (enzyme)
networks can also be obtained.
Molecular relations
The binary relations of successive enzymes are also extracted from the KEGG
metabolic pathway diagrams. They form a class of molecular relation data in KEGG.
Another important class of molecular relation is the protein-protein interactions in
regulatory pathways such as in signal transduction, cell cycle, and developmental
pathways. These data are not yet well organized, except for a few attempts in BRITE
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