Pattern recognition method zeroes in on genes that regulate cell's genetic...( >Each microarray provides a huge am...)

> "Each microarray provides a huge amount of data, and it's very difficult to extract meaningful information from it by eye," Koller said. "Over the past few years, many computational methods have been developed for dealing with this problem." Such methods identify related clusters of a handful or several dozen genes from the resulting data.

The new approach described in Nature Genetics also finds clusters, but it is the first to incorporate data about known and putative regulatory genes and the first to simultaneously predict which gene or genes regulate each cluster.

In response to internal or external signals, regulatory genes tell clusters of genes to turn on or offin other words, to start or stop making proteins. The proteins from each gene cluster, in turn, are responsible for a different cell process. These processes include converting sugar to energy, responding to stress, folding proteins, and building cellular components such as the nucleus.

Kollers pattern recognition technique builds on statistical models and the widely used technology of relational databases to look for patterns across many different data sources, such as microarray data, DNA sequence data or protein-protein interaction data. The generality of the method lets the researchers assemble data sets like Lego blocks, plugging a new database into the relational structure and letting the algorithm go to work. To make the results of this type of analysis more accessible to biologists, Koller's group has developed the GeneXPress visualization and exploration tool, freely available on the web.

"Knowing the control mechanism for gene clusters is crucial for understanding how cells respond to internal and external signals," said team member David Botstein, a professor of genetics at Stanford. "This new computational method efficiently generates targets for testing and proposes hypotheses about their regulatory roles that can be experimentally confirmed."

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Contact: David Hart
dhart@nsf.gov
703-292-7737
National Science Foundation
12-May-2003

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