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 'Neuron-reading' nanowires could accelerate development of drugs for neurological diseases
12.04.2017 | University of California - San Diego

nachricht PET radiotracer design for monitoring targeted immunotherapy
10.04.2017 | Society of Nuclear Medicine

All articles from Medical Engineering >>>

The most recent press releases about innovation >>>

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

Im Focus: Making lightweight construction suitable for series production

More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.

Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...

Im Focus: Wonder material? Novel nanotube structure strengthens thin films for flexible electronics

Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.

"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...

Im Focus: Deep inside Galaxy M87

The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.

Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...

Im Focus: A Quantum Low Pass for Photons

Physicists in Garching observe novel quantum effect that limits the number of emitted photons.

The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...

Im Focus: Microprocessors based on a layer of just three atoms

Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.

Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Expert meeting “Health Business Connect” will connect international medical technology companies

20.04.2017 | Event News

Wenn der Computer das Gehirn austrickst

18.04.2017 | Event News

7th International Conference on Crystalline Silicon Photovoltaics in Freiburg on April 3-5, 2017

03.04.2017 | Event News

 
Latest News

DGIST develops 20 times faster biosensor

24.04.2017 | Physics and Astronomy

Nanoimprinted hyperlens array: Paving the way for practical super-resolution imaging

24.04.2017 | Materials Sciences

Atomic-level motion may drive bacteria's ability to evade immune system defenses

24.04.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>