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 Zap! Graphene is bad news for bacteria
23.05.2017 | Rice University

nachricht Discovery of an alga's 'dictionary of genes' could lead to advances in biofuels, medicine
23.05.2017 | University of California - Los Angeles

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Turmoil in sluggish electrons’ existence

An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.

We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...

Im Focus: Wafer-thin Magnetic Materials Developed for Future Quantum Technologies

Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.

Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...

Im Focus: World's thinnest hologram paves path to new 3-D world

Nano-hologram paves way for integration of 3-D holography into everyday electronics

An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...

Im Focus: Using graphene to create quantum bits

In the race to produce a quantum computer, a number of projects are seeking a way to create quantum bits -- or qubits -- that are stable, meaning they are not much affected by changes in their environment. This normally needs highly nonlinear non-dissipative elements capable of functioning at very low temperatures.

In pursuit of this goal, researchers at EPFL's Laboratory of Photonics and Quantum Measurements LPQM (STI/SB), have investigated a nonlinear graphene-based...

Im Focus: Bacteria harness the lotus effect to protect themselves

Biofilms: Researchers find the causes of water-repelling properties

Dental plaque and the viscous brown slime in drainpipes are two familiar examples of bacterial biofilms. Removing such bacterial depositions from surfaces is...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

AWK Aachen Machine Tool Colloquium 2017: Internet of Production for Agile Enterprises

23.05.2017 | Event News

Dortmund MST Conference presents Individualized Healthcare Solutions with micro and nanotechnology

22.05.2017 | Event News

Innovation 4.0: Shaping a humane fourth industrial revolution

17.05.2017 | Event News

 
Latest News

Scientists propose synestia, a new type of planetary object

23.05.2017 | Physics and Astronomy

Zap! Graphene is bad news for bacteria

23.05.2017 | Life Sciences

Medical gamma-ray camera is now palm-sized

23.05.2017 | Medical Engineering

VideoLinks
B2B-VideoLinks
More VideoLinks >>>