Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Bioinformatic reconstruction of global networks provides shortcuts to protein functions

15.06.2009
Researchers at the Stockholm Bioinformatics Center in Sweden have developed bioinformatic methods for reconstructing global networks of proteins and genes that interact with each other functionally.

Eight different types of large-scale genomic, proteomic, and functional genetic data have been combined in the largest reconstructions ever of networks in nine different species. The work is published in the June issue of the journal Genome Research, and the networks are available to researchers and others via a Web-based database.

The database, developed by Professor Erik Sonnhammer's research team, is called FunCoup, which refers to the functional link between genes/proteins. This link can vary in nature - either direct physical contact, members of a complex, or members of a certain biological process. Mapping biological processes in the form of networks can be seen as the next step following the identification of all genes and the basic classification of their biochemical functions. Each gene and protein exercises its function through interactions with other molecules, usually other proteins or genes. These are the interactions that FunCoup can predict.

"The advantage of combining different types of data is that they complement each other. All forms of experiments have specific weaknesses, but by using a combination strategy, we can obtain an overall picture with better coverage," says Erik Sonnhammer.

Even though FunCoup is based on data that are publically available, in practice it is not possible for an individual researcher to process the data the way SBC does.

"For instance, we calculate the correlation in protein expression across hundreds of experiments between all pairs of proteins in a species. There are some 200 million pairs in human alone. Huge amounts of correlations and other indicators are analyzed statistically in order to translate a raw signal into a unit of functional coupling. A unique feature of FunCoup is that the type of link is predicted, for example, that 'member of complex' may be more probable than 'direct physical contact.' What's more, the networks in several species are analyzed simultaneously in order to determine whether the process is captured in model organisms," says Erik Sonnhammer.

The article in the journal Genome Research shows, for instance, how FunCoup predicts new genes in Alzheimer's, Parkinson's, and cancer.

"We hope that many scientists will discover additional relevant genes in FunCoup for their research. Biomedical researchers are often familiar with only a small number of genes that are important in a disease, and they put all their resources into these. They should more often broaden their perspectives to include other genes that are close by in the network," says Erik Sonnhammer.

The database, together with tools for analyzing networks surrounding any particular genes, is available at http://FunCoup.sbc.su.se/

Further information:
Erik Sonnhammer, professor of bioinformatics, Stockholm Bioinformatics Center, Stockholm University, phone: +46 (0)8-55378567; cell phone: +46 (0)70-5586395, e-mail Erik.Sonnhammer@sbc.su.se, home page http://sonnhammer.sbc.su.se

Maria Sandqvist | idw
Further information:
http://FunCoup.sbc.su.se/
http://sonnhammer.sbc.su.se

More articles from Life Sciences:

nachricht Researchers uncover protein-based “cancer signature”
05.12.2016 | Universität Basel

nachricht The Nagoya Protocol Creates Disadvantages for Many Countries when Applied to Microorganisms
05.12.2016 | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

Im Focus: Molecules change shape when wet

Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water

In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

NASA's AIM observes early noctilucent ice clouds over Antarctica

05.12.2016 | Earth Sciences

Shape matters when light meets atom

05.12.2016 | Physics and Astronomy

Researchers uncover protein-based “cancer signature”

05.12.2016 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>