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.

Related Articles


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 November 26, 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 November 26, 2014).

Share This


More From ScienceDaily



More Health & Medicine News

Wednesday, November 26, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Pet Dogs to Be Used in Anti-Ageing Trial

Pet Dogs to Be Used in Anti-Ageing Trial

Reuters - Innovations Video Online (Nov. 26, 2014) Researchers in the United States are preparing to discover whether a drug commonly used in human organ transplants can extend the lifespan and health quality of pet dogs. Video provided by Reuters
Powered by NewsLook.com
Today's Prostheses Are More Capable Than Ever

Today's Prostheses Are More Capable Than Ever

Newsy (Nov. 26, 2014) Advances in prosthetics are making replacement body parts stronger and more lifelike than they’ve ever been. Video provided by Newsy
Powered by NewsLook.com
From Popcorn To Vending Snacks: FDA Ups Calorie Count Rules

From Popcorn To Vending Snacks: FDA Ups Calorie Count Rules

Newsy (Nov. 25, 2014) The US FDA is announcing new calorie rules on Tuesday that will require everywhere from theaters to vending machines to include calorie counts. Video provided by Newsy
Powered by NewsLook.com
Daily Serving Of Yogurt Could Reduce Risk Of Type 2 Diabetes

Daily Serving Of Yogurt Could Reduce Risk Of Type 2 Diabetes

Newsy (Nov. 25, 2014) Need another reason to eat yogurt every day? Researchers now say it could reduce a person's risk of developing type 2 diabetes. 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:

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

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