Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Genetic data crunching achieves milestone at Stanford

21.10.2004


The revolution was not televised.



In the fall of 1999, the Stanford Microarray Database booted up, and a level of computing power was suddenly available to the field of molecular biology that only a few years earlier was inconceivable. On Oct. 19, the 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, took molecular biology by storm. They’re small slides spotted with fixed samples of DNA, each for a different gene. When a researcher prepares a labeled cell extract and incubates it with the slide, messengers in the sample stick to the fixed DNA, showing which genes in the sample are active. 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.


The problem, however, is that experiments with microarrays yield vast amounts of data. "Microarrays allow researchers to do in six months what previously would have taken six years of concerted effort," explained Gavin Sherlock, PhD, assistant research professor in genetics, who has been involved in the Stanford database from the beginning.

The need for the university database became apparent in the late 1990s after Brown and David Botstein, PhD, former chair of the genetics department, had put together a database for their own microarray results. They soon found that they needed something more sophisticated. Efficient processing and storing of microarray data, as well as the ability to easily retrieve and compare data with other experiments were all required. New information about genes spotted on the slides is continuously discovered and needs to be incorporated into data from previous experiments. In late 1999 Botstein and Brown received a grant from the National Cancer Institute for a completely revamped database, and by April 2000 all 5,000 experiments from the old database had been transferred to the new database, officially known as the Stanford Microarray Database.

Since then, researchers have used data in 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 (more are added as needed), and he believes it to be the world’s largest academic microarray database. About 200 papers have been published by Stanford researchers based on its data and many more by other groups reanalyzing Stanford data.

About one-quarter to one-third of all publicly available microarray data in the world is in the Stanford system, Sherlock said. Most of the database’s experiments are not yet public; results are available only to Stanford researchers and their collaborators until an article using the data is published in a journal. It is growing at a rapid pace, with nearly 1,000 experiments being added to the database every month.

Statistics like these - combined with Stanford’s invention of the microarray and the nine-person team devoted to maintaining the database - make Stanford a natural leader in the field. Several years ago the team made the database’s source code publicly available, and Catherine Ball, PhD, the director of the Stanford Microarray Database, serves as president of the Microarray Gene Expression Database Society, an international group working to implement standards for such work with microarrays.

"It’s much less scary to be doing microarrays at Stanford than anywhere else," Ball said. "In fact, if you’re not, you have to explain why." It’s not only a result of Stanford’s long history with microarrays, she said. "Anyone on campus was able to walk in and ask a postdoc in the Brown-Botstein lab, ’Can you please help me get this started in my lab?’" she explained. "Just having a team with expertise, enthusiasm and a cooperative nature has made this university much more likely to use microarray technology than anyplace else."

M.A. Malone | EurekAlert!
Further information:
http://www.stanford.edu.

More articles from Life Sciences:

nachricht Could this protein protect people against coronary artery disease?
17.11.2017 | University of North Carolina Health Care

nachricht Microbial resident enables beetles to feed on a leafy diet
17.11.2017 | Max-Planck-Institut für chemische Ökologie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

Im Focus: Novel Nano-CT device creates high-resolution 3D-X-rays of tiny velvet worm legs

Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.

During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....

Im Focus: Researchers Develop Data Bus for Quantum Computer

The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.

Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...

Im Focus: Wrinkles give heat a jolt in pillared graphene

Rice University researchers test 3-D carbon nanostructures' thermal transport abilities

Pillared graphene would transfer heat better if the theoretical material had a few asymmetric junctions that caused wrinkles, according to Rice University...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

NASA detects solar flare pulses at Sun and Earth

17.11.2017 | Physics and Astronomy

NIST scientists discover how to switch liver cancer cell growth from 2-D to 3-D structures

17.11.2017 | Health and Medicine

The importance of biodiversity in forests could increase due to climate change

17.11.2017 | Studies and Analyses

VideoLinks
B2B-VideoLinks
More VideoLinks >>>