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Stanford/Packard scientist's data-mining technique strikes genetic gold

A new method to mine existing scientific data may provide a wealth of information about the interactions among genes, the environment and biological processes, say researchers at the Stanford University School of Medicine, Lucile Packard Children's Hospital and Harvard Medical School. Like panning for gold, they used the powerful technique to sift through millions of bits of unrelated information - in this case, gene expression data from so-called microarray experiments - to pinpoint genes likely to be involved in leukemia, aging, injury and muscle development.

"This is just the tip of the iceberg," said bioinformatics specialist Atul Butte, MD, PhD, who is also a pediatrician at Lucile Packard Children's Hospital at Stanford. "Nearly 100 different diseases have been studied using microarrays, spanning all of medicine. This is a new way to explore this type of data. We can study virtually everything that's been studied." Butte is the first author of the study, which is published in the Jan. 6 online issue of Nature Biotechnology.

The advance comes with a caveat, however: clinically useful nuggets will be buried under the avalanche of data inundating international repositories each year unless scientists come up with a way to better classify their experiments and results.

"Libraries figured out a long time ago how to classify items using the Dewey decimal and other systems," said Butte, who estimates that the contents of the databases are more than doubling each year. "We need to write software now that will help scientists assign the proper concepts to each experiment."

Microarray experiments allow researchers to compare the expression patterns of tens of thousands of individual genes over time in diseased and healthy cells, or in many other experimental conditions. Each experiment generates thousands of pieces of data about the cell's genes. Although biologists use the technology routinely, focusing only on the few results pertinent t
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Source:Stanford University Medical Center


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