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 3-D visualization of the pancreas -- new tool in diabetes research
15.03.2017 | Umea University

nachricht New PET radiotracer identifies inflammation in life-threatening atherosclerosis
02.03.2017 | 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: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>