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Primeur weekly 2016-10-10

Exascale supercomputing

The incredible shrinking particle accelerator ...

Brookhaven Lab to play major role in 2 DOE exascale computing application projects ...

Quantum computing

More stable qubits in perfectly normal silicon ...

Focus on Europe

RSC supercomputers go West ...

Hardware

Allinea tools play vital role in advancing computational research at the VSC, Austria's largest HPC facility ...

Smallest transistor ever ...

Turning to the brain to reboot computing ...

Complex materials can self-organize into circuits, may form basis for multifunction chips ...

Wireless data centre on a chip aims to cut energy use ...

Adapteva announces 28nm 64-core Epiphany-IV microprocessor chip ...

SGI introduces unique scale-out solution for SAP HANA that protects investments when moving to real-time business ...

Applications

Clemson University scientists receive $1.8 million grant to combat Type 2 diabetes ...

Climate change intensifies night-time storms over Lake Victoria ...

Computer simulations explore how Alzheimer's disease starts ...

Rice University lab explores cement's crystalline nature to boost concrete performance ...

Rice University researchers say 2D boron may be best for flexible electronics ...

Large animals, such as the imperious African elephant, most vulnerable to impact of human expansion ...

Computer simulation finds dangerous molecule activity for ageing ...

Tornadogenesis ...

As hurricane heads up coast, a RENCI supercomputer swings into action ...

New drug candidate may reduce deficits in Parkinson's disease ...

XSEDE allocations awarded to 155 research teams across U.S. ...

OSC part of NSF-funded consortium for advancing research computing practices ...

NCSA awarded NSF grant to expand computational science education in food, energy, and water ...

Crosstalk analysis of biological networks for improved pathway annotation ...

The Cloud

Nimbix collaborates with IBM and NVIDIA to launch powerful GPU Cloud offering ...

Crosstalk analysis of biological networks for improved pathway annotation

27 Sep 2016 Stockholm - Researchers at Stockholm University and Science for Life Laboratory have developed a new computer algorithm for analysing gene function called BinoX, which was e-published inNucleic Acids Researchon September 22, Ogris et al., 2016a. The method, developed by Professor Erik Sonnhammer's research group, associates experimentally derived gene lists and known pathways. It does this in a new way, by employing a large gene network and determining if a gene list and a pathway has more network links than expected, using the binomial distribution. This is a significant advance over previous methods, and as a result BinoX yields substantially better accuracy. In particular, the improvement compared to the commonly used gene overlap enrichment method is massive; the sensitivity was benchmarked to increase by more than 60 times at the same time as the false positive rate was reduced to zero.

The paper demonstrates how BinoX can be used to find many biologically meaningful pathway annotations for gene sets from cancer and other diseases, which are not found by other methods.

"We believe that our new method will revolutionise the way researchers do pathway analysis and yield many new functional insights. The tools commonly used today are based on the gene overlap method which is very limited and unreliable. It often fails to find activated pathways, yet it often finds incorrect pathways. The reason for this is that it applies a statistical method to very sparse data that violate its statistical assumptions", stated Erik Sonnhammer.

To make BinoX directly usable for other researchers, a public web server (Ogris et al., 2016b) was set up for on-line pathway analysis of single gene sets, which applies the BinoX algorithm to all KEGG pathways and FunCoup networks. The FunCoup network database of functional couplings between genes and gene products was also developed by Erik Sonnhammer's group. It currently contains comprehensive networks for human and 10 model organisms. For instance, the human network consists of over 18,000 genes/proteins connected to each other with over 4 million links.

"BinoX works so well thanks to the high density of the FunCoup networks, which makes it possible to find many functional network links between gene sets, even if they have no shared genes. This gives statistical power and makes it possible to find statistically significant enrichment of crosstalk", stated Erik Sonnhammer.

Ogris C., Guala D., Helleday T. and Sonnhammer E.L.L. are the authors of the paper titled "A Novel Method for Crosstalk Analysis of Biological Networks: Improving accuracy of Pathway Annotation", published in

Ogris C., Helleday T. and Sonnhammer E.L.L. are the authors of the paper titled "PathwAX: a web server for network crosstalk based pathway annotation", published in

More information is available at http://nar.oxfordjournals.org/content/early/2016/09/22/nar.gkw849.full.pdf+html .
Source: Stockholm University

Back to Table of contents

Primeur weekly 2016-10-10

Exascale supercomputing

The incredible shrinking particle accelerator ...

Brookhaven Lab to play major role in 2 DOE exascale computing application projects ...

Quantum computing

More stable qubits in perfectly normal silicon ...

Focus on Europe

RSC supercomputers go West ...

Hardware

Allinea tools play vital role in advancing computational research at the VSC, Austria's largest HPC facility ...

Smallest transistor ever ...

Turning to the brain to reboot computing ...

Complex materials can self-organize into circuits, may form basis for multifunction chips ...

Wireless data centre on a chip aims to cut energy use ...

Adapteva announces 28nm 64-core Epiphany-IV microprocessor chip ...

SGI introduces unique scale-out solution for SAP HANA that protects investments when moving to real-time business ...

Applications

Clemson University scientists receive $1.8 million grant to combat Type 2 diabetes ...

Climate change intensifies night-time storms over Lake Victoria ...

Computer simulations explore how Alzheimer's disease starts ...

Rice University lab explores cement's crystalline nature to boost concrete performance ...

Rice University researchers say 2D boron may be best for flexible electronics ...

Large animals, such as the imperious African elephant, most vulnerable to impact of human expansion ...

Computer simulation finds dangerous molecule activity for ageing ...

Tornadogenesis ...

As hurricane heads up coast, a RENCI supercomputer swings into action ...

New drug candidate may reduce deficits in Parkinson's disease ...

XSEDE allocations awarded to 155 research teams across U.S. ...

OSC part of NSF-funded consortium for advancing research computing practices ...

NCSA awarded NSF grant to expand computational science education in food, energy, and water ...

Crosstalk analysis of biological networks for improved pathway annotation ...

The Cloud

Nimbix collaborates with IBM and NVIDIA to launch powerful GPU Cloud offering ...