Databases and Systems

Introduction
5 KEGG: FROM GENES TO
BIOCHEMICAL PATHWAYS
Minoru Kanehisa
Institute for Chemical Research, Kyoto University, Kyoto,
Japan
Molecular biology has been a discipline dominated by the reductionistic approach
where starting from a specific functional aspect of a biological organism the genes
and proteins that are responsible for the function are searched and characterized. In
contrast, the complete set of genes and gene products that has become available by
the whole genome sequencing is a starting point of an alternative approach, which
may be called a synthetic approach, toward understanding how genes and molecules
are networked to form a biological system. While it is unlikely that the reductionistic
approach alone can cover the entire aspects of the biological system, the synthetic
approach has a potential to provide a complete picture because the starting set of
building blocks is complete. In reality, however, the complete genome sequence does
not tell much about how the organism functions as a biological system. This is not
only because we do not yet have appropriate means to interpret the sequence data,
but also because all the information to build up a biological system may not be
present in the genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is an effort to make links
from the gene catalogs generated by the genome sequencing projects to the
biochemical pathways that may be considered wiring-diagrams of genes and
molecules [ 1]. Specifically, the objectives of KEGG are the following:
1. to computerize all aspects of cellular functions in terms of the pathway of
interacting molecules or genes,
2.
to maintain gene catalogs for all organisms and link each gene product to a
pathway component,