Stanford's Great Big Data Mountain

By Shawna Williams

	Catherine Ball, PhD, director of the Stanford Microarray Database, and Gavin Sherlock, PhD, assistant research professor in genetics. Photo: Steve Gladfelter

When famed criminal Willie Sutton was asked why he robbed banks, he answered, “Because that’s where the money is.” A similar line of reasoning could apply to scientists who want to do microarray research at Stanford: That’s where the information is.

In October, 2004, the Stanford Microarray Database recorded its 50,000th experiment, marking its place at the forefront of an information processing revolution that has yielded groundbreaking insights into the relationships between genes and illness, as well as fundamental biological discoveries.

Microarrays — developed in the lab of biochemistry professor Patrick Brown, MD, PhD, in the early 1990s — are small slides spotted with fixed samples of DNA, each for a different gene. When a labeled cell extract is incubated with the slide, messengers in the sample stick to the fixed DNA, showing which genes in the sample are active.

Detecting Change

Microarrays are especially useful for comparisons between normal and cancerous tissues or between different stages of development. Researchers use them to nose out the genes associated with such changes.

“Microarrays allow researchers to do in six months what previously would have taken six years of concerted effort,” says Gavin Sherlock, PhD, assistant professor (research) of genetics, who has been involved in the Stanford database from the beginning.

However, experiments with microarrays yield vast amounts of data. Brown and David Botstein, PhD, former chair of the genetics department, began assembling a database for their own microarray results in the late 1990s and soon found they needed something more sophisticated to easily retrieve data and compare it with other experiments.

A grant from the National Cancer Institute enabled Botstein and Brown to revamp the database, and by April 2000 all 5,000 experiments from the old system had been transferred to the new system.

Since then, researchers have used the database to illuminate everything from cell division in yeast to cancer-causing genes to what happens to bacteria when they’re deprived of iron. Microarray data have also allowed scientists to understand how various drugs affect the malaria bug, to find out what the immune system attacks in patients with autoimmune diseases and to pinpoint genes involved in multiple sclerosis.

Sherlock estimates the database now supports 400 campus researchers doing work on 30 different organisms, and he believes it to be the world’s largest academic microarray database.

About one-quarter to one-third of all publicly available microarray data in the world is in the Stanford system, Sherlock says. It is growing at a rapid pace, with nearly 1,000 experiments being added every month.

In recent years, the Stanford Microarray Database has played a leading role in establishing internationally accepted standards for the annotation and sharing of microarray data. Highly accessible and user-friendly, it is today the most widely used DNA microarray database in the world.

The breadth and depth of Stanford’s experience with microarrays make it a natural leader in the field. “It’s much less scary to be doing microarrays at Stanford than anywhere else,” says Catherine Ball, PhD, director of the Stanford Microarray Database. “In fact, if you’re not, you have to explain why.”