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PUBLIC RELEASE DATE:
15-Feb-2003

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Contact: Sara Selis
selis@stanford.edu
Stanford University Medical Center
@sumedicine

Stanford researcher advocates far-reaching microarray data exchange

DENVER, Co- Gene microarrays have become an increasingly important tool in biomedical research, allowing scientists to see complex patterns of gene expression inside particular cells. The result is a better understanding of different types of cancer and other diseases.

But as the number of gene microarrays performed in experiments has multiplied, the task of storing, organizing and analyzing the resulting data has become increasingly daunting. This has spurred the development of microarray databases - sophisticated repositories that not only give researchers a way to safely store their data, but also provide tools to analyze it.

Gavin Sherlock, PhD, director of the Stanford Microarray Database at Stanford University Medical Center, will discuss the history of gene microarray databases and the current movement - in which he is active - to establish standards for the open publication and exchange of microarray data. His presentation will take place Saturday during the Databases and Data Sharing program at the annual meeting of the American Association for the Advancement of Science in Denver.

When gene microarray experiments were first performed in 1995, researchers used relatively few samples and there were fewer genes represented on the microarrays. Scientists could therefore analyze the resulting data using primitive spreadsheets and custom-written, one-time scripts. But as experiments began to involve more microarrays, "researchers were dealing with massive amounts of data and it became obvious that they needed a more sophisticated way to organize it," Sherlock said. Responding to this need, a group of genetics researchers at Stanford developed the first gene microarray database in 1997.

Since then, a crop of such databases has sprung up, including about a dozen commercially run databases and a handful of open-source databases developed at academic institutions.

These databases are becoming even more important, Sherlock explained, with the current movement to make microarray data used in published research publicly available so other scientists can analyze it and replicate the research. A recently established database in England called Array-Express aims to serve as an international repository for such data.

But the movement to share microarray data in this fashion depends on the use of a common standard by which all users have easy access. A group of researchers known as the Microarray Gene Expression Data group has established such a standard, known as Minimal Information About a Microarray Experiment. The journal Nature recently agreed to adopt this format for all its published research, meaning any researcher whose results were derived from gene microarrays must submit the raw microarray data to a common database - in this case, to Array Express. Sherlock said Nature's move is a significant step that will drive the evolution of microarray databases, and he hopes other journals will soon follow suit.

"The development of these standards is extremely important to the future of database development," Sherlock said. "As the standards get nailed down, the databases will have to catch up and accommodate them."

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Stanford University Medical Center integrates research, medical education and patient care at its three institutions - Stanford University School of Medicine, Stanford Hospital & Clinics and Lucile Packard Children's Hospital at Stanford. For more information, please visit the Web site of the medical center's Office of Communication & Public Affairs at http://mednews.stanford.edu.


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