Featured Research

from universities, journals, and other organizations

Gene expression databases could uncover therapeutic targets, biological processes

Date:
October 1, 2013
Source:
Carnegie Mellon University
Summary:
A new computational tool developed by US and Israeli scientists will help scientists exploit the massive databases of gene expression experimental results that have been created over the past decade. Researchers say it could uncover new links between diseases and treatments and provide new insights into biological processes.

A new computational tool developed by U.S. and Israeli scientists will help scientists exploit the massive databases of gene expression experimental results that have been created over the past decade. Researchers say it could uncover new links between diseases and treatments and provide new insights into biological processes.

Related Articles


The team, headed by Ziv Bar-Joseph of Carnegie Mellon University, reports in the October issue of the journal Nature Methods that the tool, called ExpressionBlast, enables searches based directly on experimental values, rather than keywords.

The researchers already have used ExpressionBlast to uncover intriguing clues about SIRT6, the first gene shown to extend lifespan in mice and thus a potentially important drug target. By mining experimental data stored in a public repository called the Gene Expression Omnibus (GEO) maintained by the National Center for Biotechnology Information, they found that SIRT6 may be involved with functions that include immune response, metabolism and the regulation of gender-specific genes.

"Because so little is known about SIRT6, it would be difficult to search the hundreds of thousands of GEO datasets using keywords and, without other guidance, it would be practically impossible to find other experiments with gene expression patterns similar to SIRT6," said Bar-Joseph, an associate professor of computational biology and machine learning. "ExpressionBlast enabled us to take SIRT6 gene expression data from just two mouse experiments and find other experimental data in GEO with similar expression patterns."

The tool is available online. The search engine enables researchers to search for expression patterns that are similar or opposite to their own results and can search within and across species.

Guy Zinman, Shoshana Naiman, Yariv Kanfi and Haim Cohen of Bar-Ilan University worked with Bar-Joseph to develop ExpressionBlast and are co-authors of the journal report. Their intention was to develop a tool for gene expression queries that would be the equivalent of Blast, a two-decade-old tool for searching gene sequence databases that remains one of the most widely used tools in bioinformatics.

Genes encode the information necessary for life, while gene expression is the process by which that genetic information is transformed into proteins and by which genes are regulated. Understanding gene expression thus is critical for understanding biological and disease processes. This information is so important that, for the past decade or so, most leading journals have required researchers who publish papers on gene expression to submit their experimental data to public repositories such as GEO.

GEO alone holds data from more than 1 million microarrays. Each of these microarrays might contain up to 40,000 numerical values -- which indicate which genes are over -- or underexpressed, and by how much. GEO and the European Bioinformatics Institute's ArrayExpress thus represent a treasure trove of potential discoveries. But existing searches are often dependent on keyword summaries submitted by each researcher, or require manual comparisons of microarrays.

ExpressionBlast uses novel, automated and scalable text analysis algorithms to transform the unstructured data in GEO so that it can be systematically searched. The researchers have thus far processed tens of thousands of expression series representing hundreds of thousands of individual arrays across several species. Once processed in this way, the data can be accessed easily via a graphical interface.


Story Source:

The above story is based on materials provided by Carnegie Mellon University. Note: Materials may be edited for content and length.


Journal Reference:

  1. Guy E Zinman, Shoshana Naiman, Yariv Kanfi, Haim Cohen, Ziv Bar-Joseph. ExpressionBlast: mining large, unstructured expression databases. Nature Methods, 2013; 10 (10): 925 DOI: 10.1038/nmeth.2630

Cite This Page:

Carnegie Mellon University. "Gene expression databases could uncover therapeutic targets, biological processes." ScienceDaily. ScienceDaily, 1 October 2013. <www.sciencedaily.com/releases/2013/10/131001192153.htm>.
Carnegie Mellon University. (2013, October 1). Gene expression databases could uncover therapeutic targets, biological processes. ScienceDaily. Retrieved December 18, 2014 from www.sciencedaily.com/releases/2013/10/131001192153.htm
Carnegie Mellon University. "Gene expression databases could uncover therapeutic targets, biological processes." ScienceDaily. www.sciencedaily.com/releases/2013/10/131001192153.htm (accessed December 18, 2014).

Share This


More From ScienceDaily



More Health & Medicine News

Thursday, December 18, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Kids Die While Under Protective Services

Kids Die While Under Protective Services

AP (Dec. 18, 2014) As part of a six-month investigation of child maltreatment deaths, the AP found that hundreds of deaths from horrific abuse and neglect could have been prevented. AP's Haven Daley reports. (Dec. 18) Video provided by AP
Powered by NewsLook.com
UN: Up to One Million Facing Hunger in Ebola-Hit Countries

UN: Up to One Million Facing Hunger in Ebola-Hit Countries

AFP (Dec. 17, 2014) Border closures, quarantines and crop losses in West African nations battling the Ebola virus could lead to as many as one million people going hungry, UN food agencies said on Wednesday. Duration: 00:52 Video provided by AFP
Powered by NewsLook.com
When You Lose Weight, This Is Where The Fat Goes

When You Lose Weight, This Is Where The Fat Goes

Newsy (Dec. 17, 2014) Can fat disappear into thin air? New research finds that during weight loss, over 80 percent of a person's fat molecules escape through the lungs. Video provided by Newsy
Powered by NewsLook.com
Why Your Boss Should Let You Sleep In

Why Your Boss Should Let You Sleep In

Newsy (Dec. 17, 2014) According to research out of the University of Pennsylvania, waking up for work is the biggest factor that causes Americans to lose sleep. 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