Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Researchers Develop Promising New Gene Network Analysis Method

09.05.2005


Compared with a long-used linear model, a correlation-based statistical method is a more reliable way to map complex gene interactions and pinpoint genes that may be potential cancer treatment targets, according to new Brown University research.



The research is important because it describes a promising new tool for tracing human gene connections, a task critical for understanding and treating cancer and other diseases. Results appeared this week in the online edition of the Proceedings of the National Academy of Sciences. “Genes influence one another in many intricate ways,” said Leon Cooper, professor of physics and neuroscience and director of the Institute for Brain and Neural Systems at Brown. “What we need is a map, or network, of these links. What we’ve identified in this project is a more effective method for making this map.”

The research team – which included scientists from the fields of biology, physics, statistics and computer science at Brown, Università di Bologna in Italy and Tel Aviv University in Israel – set out to answer a question. When a deadly “oncoprotein” is switched on, what chain reaction of gene activity does it set off?


The protein, c-Myc, causes cells to multiply. If the protein is produced unchecked, it can cause breast, colon and other types of cancer. C-Myc contributes to more than 70,000 deaths in the United States each year.

Once the c-Myc switch is thrown, thousands of other genes start pumping out proteins or switching on other genes, which activates still more genes. One way to study this web of connections would be to set off the chain reaction and study it over time. To make that happen, Brown researchers came up with a clever experiment.

John Sedivy, a long-time c-Myc researcher and the director of Brown’s Center for Genomics and Proteomics, developed rat cells that lacked the c-Myc gene. These cells were further modified to make a form of the c-Myc protein, which could be switched on or off by the hormone treatment tamoxifen.

One batch of cells was treated with tamoxifen, then harvested one, two, four, eight and 16 hours later. Another batch of cells didn’t get the drug but were harvested during the same time frame.

Analysis of gene activity generated in the experiments revealed 1,191 possible players in the c-Myc gene network. A statistical team, led by Gastone Castellani, an associate research professor with the Institute for Brain and Neural Systems and a professor at the Università di Bologna, tested two methods to try to model this network.

One was the linear Markov model, a decades-old tool used to crunch everything from sports statistics to language production. The other was a correlation method based on network theory, which has been used to explain complex systems such as power grids and neural networks.

After applying both statistical methods to the experimental data, the team found that the correlation method was a more effective analytical tool. The method was sensitive enough to capture gene network changes after tamoxifen treatment, producing a list of 130 genes significantly altered by c-Myc activation. This method was also reliable. When researchers reshuffled the data time points, those network changes disappeared.

In contrast, the gene network constructed by the linear Markov model appeared to be insensitive to the effects of tamoxifen. Even when researchers shuffled the data time points, the network appeared largely unchanged.

“Network theory has been hugely informative in analyzing the genomes of simple species such as yeast,” Sedivy said. “Here, the theory is applied to a much more complex system: humans. The overall concept – the time series experiments and the combination of statistics and network theory – is quite novel. This should be an important new approach to studying gene expression.”

The research team also includes Brenda O’Connell and Nicola Neretti from Brown University; Daniel Remondini from Università di Bologna; and Nathan Intrator, who holds positions at Brown University and Tel Aviv University.

The National Institutes of Health, the Ministero dell’Instruzione, dell’Università e della Ricera, the Institute for Brain and Neural Systems and the Office of the Vice President of Research at Brown University funded the work.

Wendy Lawton | EurekAlert!
Further information:
http://www.brown.edu

More articles from Life Sciences:

nachricht A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>