SITE VISIT: Gene Wiring Diagrams

Science  03 Apr 1998:
Vol. 280, Issue 5360, pp. 7a
DOI: 10.1126/science.280.5360.7a

Genome projects do a great job of providing a gene's sequence and protein product, but ask them for functional info—what that protein does in the cell—and you're likely to come up empty. Helping to fill the gap is the Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.ad.jp/kegg/), a site that aims to make sense of the flood of sequencing data by linking genes to biochemical pathways.

Launched in 1995 as part of Japan's national genome program, KEGG—based at the Institute for Chemical Research, Kyoto University—holds molecular and gene catalogs for all known compounds in living cells, along with some 100 maps of metabolic and regulatory pathways. It also contains genome maps—viewable with the Java miniprograms known as “applets”—for the world's genome projects. And KEGG links into protein and gene databases such as SWISS-PROT and GenBank. Searching for “alcohol dehydrogenase,” for example, pulls up maps showing the enzyme's position in five metabolic processes, or its gene's sequence in the rat genome. Especially useful, says KEGG leader Minoru Kanehisa, is that you can feed in several genes or enzymes and find out what pathways connect them. That makes KEGG a biological “wiring-diagram database,” he explains.

Bioinformatics expert Chris Sander of Millennium Pharmaceuticals in Cambridge, Massachusetts, calls KEGG “the most comprehensive and easily accessible” metabolic pathway database; unlike many such ventures, he says, “it has a good chance of surviving.” This year, Kanehisa expects to add more regulatory pathways and fill out gene information on higher organisms.

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