Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Deeper than ancestry.com, 'EvoCor' identifies gene relationships

04.06.2014

Virginia Tech researchers develop search engine for identifying functionally linked genes

A frontier lies deep within our cells.


Gregorio Valdez, PhD

Jim Stroup/Virginia Tech

Our bodies are as vast as oceans and space, composed of a dizzying number of different types of cells. Exploration reaches far, yet the genes that make each cell and tissue unique have remained largely obscure.

That’s changing with the help of a team led by Gregorio Valdez, an assistant professor at the Virginia Tech Carilion Research Institute.

Valdez and his team designed a search engine – called EvoCor – that identifies genes that are functionally linked.

The name, a portmanteau of “evolution” and “correlation,” points to the idea that genes with a similar evolutionary history and expression pattern have evolved together to control a specific biological process.

The project, described in May in the journal Nucleic Acids Research, may help medical scientists find ways to treat diseases that often have a genetic component, such as cancer or Alzheimer’s disease.

A scientist types the name of a gene into a search box, and EvoCor quickly sifts through the evolutionary history of all mapped genes – human and otherwise.

EvoCor then compares the expression pattern of all genes to generate a list of candidate genes that function together with the query gene to drive a cellular process – from generating more energy for the cell to clearing cellular debris. The scientist can use this list for the next stage of research.

“This platform allows researchers to generate lists of candidate genes quickly and at no cost,” Valdez said. “EvoCor should speed the discovery of complex molecular mechanisms that control key cellular processes, including those that function to regenerate axons.”

Most cellular functions — communication, division, death — result from a gene telling a cell how it’s supposed to behave.

Scientists study how a gene is expressed and functions to determine, for example, eye color. The matter becomes more complicated when multiple genes with different functions are intricately related. Therein lies the problem. A researcher may start with one gene, but needs to know what other genes might play a part in influencing a particularly complex cellular function, such as the survival of neurons.

Once the other genes are known, the scientist can strategically study their function alone and as part of the larger network of genes.

To identify candidate genes, scientists have relied on expensive and time-consuming biochemical approaches. EvoCor takes advantage of the wealth of publicly available genome and gene expression datasets to generate a list of candidate genes.

“It comes down to evolution,” said James Dittmar, a fourth-year Virginia Tech Carilion School of Medicine student who is also a member of the Valdez laboratory and the first author of the journal article. “We took advantage of nearly 200 organisms with fully sequenced genomes to map out and compare the evolutionary history of all human genes.”

Combing through the 21,000 human genes already mapped, 182 different genomes, and large gene expression datasets all maintained by the National Institutes of Health is a huge task. EvoCor makes it far more manageable.

“Scientists can now use EvoCor to take advantage of this massive amount of publicly available data to discover networks of genes without prior knowledge of their function,” Valdez said.

When scientists fully understand every gene influencing a particular cellular output, they will have more options for developing therapeutics. In his own research, Valdez hopes to discover molecules that function to slow or halt cognitive and motor impairment caused by diseases and aging.

“We know of many genes that, when mutated, lead to disastrous outcomes,” Valdez said. “But these genes don’t function alone. EvoCor identifies functional partners and those partners could turn out to be better targets for therapeutics.”

EvoCor was developed in collaboration with Lauren McIver, Pawel Michalak, and Harold “Skip” Garner, all scientists at the Virginia Bioinformatics Institute of Virginia Tech.

Valdez and his team plan to modify EvoCor further, so it can make even more powerful and specific predictions, easing the way for researchers trekking the new frontier.

Written by Ashley WennersHerron

Media contact

Paula Byron
paulabyron@vt.edu
540-526-2027

Paula Byron | Eurek Alert!
Further information:
http://research.vtc.vt.edu/news/2014/jun/02/deeper-ancestrycom-evocor-identifies-gene-relation/

Further reports about: Exploration Medicine diseases function genes mechanisms oceans

More articles from Medical Engineering:

nachricht Visualizing gene expression with MRI
23.12.2016 | California Institute of Technology

nachricht Illuminating cancer: Researchers invent a pH threshold sensor to improve cancer surgery
21.12.2016 | UT Southwestern Medical Center

All articles from Medical Engineering >>>

The most recent press releases about innovation >>>

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

Im Focus: Traffic jam in empty space

New success for Konstanz physicists in studying the quantum vacuum

An important step towards a completely new experimental access to quantum physics has been made at University of Konstanz. The team of scientists headed by...

Im Focus: How gut bacteria can make us ill

HZI researchers decipher infection mechanisms of Yersinia and immune responses of the host

Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...

Im Focus: Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.

While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...

Im Focus: Studying fundamental particles in materials

Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales

Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...

Im Focus: Designing Architecture with Solar Building Envelopes

Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.

As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Sustainable Water use in Agriculture in Eastern Europe and Central Asia

19.01.2017 | Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

 
Latest News

New Study Will Help Find the Best Locations for Thermal Power Stations in Iceland

19.01.2017 | Earth Sciences

Not of Divided Mind

19.01.2017 | Life Sciences

Molecule flash mob

19.01.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>