Featured Research

from universities, journals, and other organizations

Dealing With Reams Of Data: Scientists Work Toward Unraveling Gene Expression In The Brain

Date:
February 18, 2003
Source:
Johns Hopkins Medical Institutions
Summary:
Using Web-based tools they developed to sift through reams of data, scientists from the Kennedy Krieger Institute and Johns Hopkins hope to unravel the genetics of neurological problems associated with Down syndrome, autism and lead poisoning.

Using Web-based tools they developed to sift through reams of data, scientists from the Kennedy Krieger Institute and Johns Hopkins hope to unravel the genetics of neurological problems associated with Down syndrome, autism and lead poisoning.

Their search starts with microarrays, or so-called "gene chips," which measure the activity of tens of thousands of genes all at once. By analyzing the pattern of gene activity in brain tissue, the scientists hope to find genes that are more or less active than normal and that may, therefore, be involved in causing problems.

On Feb. 16 at the annual meeting of the American Association for the Advancement of Science, Jonathan Pevsner, Ph.D., will demonstrate how two tools they developed, called SNOMAD and DRAGON, can be used to find the needle in the haystack of microarray data. As an example, Pevsner applied the programs to microarray data from Down syndrome.

"In some conditions, like autism, the biological cause is still unclear, but even in Down syndrome, which we know is the result of having an extra copy of chromosome 21, we don't know exactly what genes or processes lead to the neurological changes," says Pevsner, associate professor of neurology at Kennedy Krieger and an associate professor of neuroscience at the Johns Hopkins School of Medicine.

While it makes sense that all chromosome 21 genes would be more active than normal in Down syndrome, no one has ever proved it. In his presentation and in an upcoming issue of the journal Genomics, Pevsner will report that using microarrays (and DRAGON) showed that, indeed, as a group, chromosome 21 genes are dramatically overexpressed.

"There's no smoking gun on chromosome 21 in our initial analysis, but further investigation might reveal specific genes that influence the severity of the condition," says Pevsner.

In addition to dealing with the complexity that comes with receiving a mountain of data from a microarray experiment, in many cases scientists interested in answering the biological question -- which genes are expressed differently -- may not have the mathematical or computational expertise to analyze and interpret the results to get an answer with meaning, notes Pevsner.

"To use microarrays effectively, you have to do both the biology and the math correctly," he says. "SNOMAD and DRAGON supplement other available analysis tools to help researchers make sense of their results. The bottom line, however, is that any result must be confirmed."

SNOMAD, or Standardization and Normalization of Microarray Data, was developed in 2001 by a graduate student in Pevsner's lab, in conjunction with Scott Zeger, Ph.D., chair of biostatistics at the Johns Hopkins Bloomberg School of Public Health. The online computer program processes researchers' microarray data to search for "signal" within the "noise" of normal variation in gene expression levels, says Pevsner.

DRAGON, or Database Referencing of Array Genes Online, ties the results of an individual microarray experiment to other available information. For example, DRAGON cross-references over- and under-expressed genes in a researcher's microarray to five online databases, identifying the genes and pulling together what is already known about their functions and roles in disease. The program can also produce visual displays of the results -- graphs, charts, drawings -- that the researcher can manipulate to see -- really see -- how the results fit together.

"Microarrays are really an exploration, and at the end of the analysis we have to decide if we believe it or not," says Pevsner. "But even with the complexities inherent in the brain, we think microarrays can help improve understanding of neurological disorders."

###

On the Web:

SNOMAD and DRAGON are available at:http://pevsnerlab.kennedykrieger.org/

The Kennedy Krieger Institutehttp://www.kennedykrieger.org


Story Source:

The above story is based on materials provided by Johns Hopkins Medical Institutions. Note: Materials may be edited for content and length.


Cite This Page:

Johns Hopkins Medical Institutions. "Dealing With Reams Of Data: Scientists Work Toward Unraveling Gene Expression In The Brain." ScienceDaily. ScienceDaily, 18 February 2003. <www.sciencedaily.com/releases/2003/02/030218090100.htm>.
Johns Hopkins Medical Institutions. (2003, February 18). Dealing With Reams Of Data: Scientists Work Toward Unraveling Gene Expression In The Brain. ScienceDaily. Retrieved August 30, 2014 from www.sciencedaily.com/releases/2003/02/030218090100.htm
Johns Hopkins Medical Institutions. "Dealing With Reams Of Data: Scientists Work Toward Unraveling Gene Expression In The Brain." ScienceDaily. www.sciencedaily.com/releases/2003/02/030218090100.htm (accessed August 30, 2014).

Share This




More Health & Medicine News

Saturday, August 30, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

3 Things To Know About The Ebola Outbreak's Progression

3 Things To Know About The Ebola Outbreak's Progression

Newsy (Aug. 29, 2014) Here are three things you need to know about the deadly Ebola outbreak's progression this week. Video provided by Newsy
Powered by NewsLook.com
Killer Amoeba Found in Louisiana Water System

Killer Amoeba Found in Louisiana Water System

AP (Aug. 28, 2014) State health officials say testing has confirmed the presence of a killer amoeba in a water system serving three St. John the Baptist Parish towns. (Aug. 28) Video provided by AP
Powered by NewsLook.com
Who Could Be Burnt by WHO's E-Cigs Move?

Who Could Be Burnt by WHO's E-Cigs Move?

Reuters - Business Video Online (Aug. 28, 2014) The World Health Organisation has called for the regulation of electronic cigarettes as both tobacco and medical products. Ciara Lee looks at the impact of the move on the tobacco industry. Video provided by Reuters
Powered by NewsLook.com
CDC Director On Ebola Outbreak: 'It's Worse Than I Feared'

CDC Director On Ebola Outbreak: 'It's Worse Than I Feared'

Newsy (Aug. 28, 2014) CDC director Tom Frieden says the Ebola outbreak is even worse than he feared. But he also said there's still hope to contain it. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins