Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New bioinformatics tool to visualize transcriptomes

10.03.2014

ZENBU, a new, freely available bioinformatics tool developed at the RIKEN Center for Life Science Technology in Japan, enables researchers to quickly and easily integrate, visualize and compare large amounts of genomic information resulting from large-scale, next-generation sequencing experiments.

Next-generation sequencing has revolutionized functional genomics, with protocols such as RNA-seq, ChIP-seq and CAGE being used widely around the world.

The power of these techniques lies in the fact that they enable the genome-wide discovery of transcripts and transcription factor binding sites, which is key to understanding the molecular mechanisms underlying cell function in healthy and diseased individuals and the development of diseases like cancer.

The integration of data from multiple experiments is an important aspect of the interpretation of results, however the growing number of datasets generated makes a thorough comparison and analysis of results cumbersome.

In a report published today in the journal Nature Biotechnology, Jessica Severin and colleagues describe the development of ZENBU, a tool that combines a genome browser with data analysis and a linked expression view, to facilitate the interactive visualization and comparison of results from large numbers of next-generation sequencing datasets.

The key difference between ZENBU and previous tools is the ability to dynamically combine thousands of experimental datasets in an interactive visualization environment through linked genome location and expression signal views.

This allows scientists to compare their own experiments against the over 6000 ENCODE and FANTOM consortium datasets currently loaded into the system, thus enabling them to discover new and interesting biological mechanisms. The tool is designed to integrate millions of experiments/datasets of any kind (RNA-seq, ChIP-seq or CAGE), hence its name: zenbu means 'all' or 'everything' in Japanese.

ZENBU is freely available for use on the web and for installation in individual laboratories, and all ZENBU sites are connected and continuously share data. The tool can be accessed or downloaded from http://fantom.gsc.riken.jp/zenbu/.

"By distributing the data and servers we encourage scientists to load and share their published data to help build a comprehensive resource to further advance research efforts and collaborations around the world," explain the authors.

###

ZENBU is accessible at http://fantom.gsc.riken.jp/zenbu/

Dr. Forrest and Dr. Severin are available for interviews in English by email. Please contact:

Alistair Forrest, Team leader
Genome Information Analysis Team
Life Science Accelerator Technology Group
Division of Genomic Technologies
RIKEN Center for Life Science Technologies
Email: forrest@gsc.riken.jp

Jessica Severin, Senior Technical Scientist
Genome Information Analysis Team
Life Science Accelerator Technology Group
Division of Genomic Technologies
RIKEN Center for Life Science Technologies
Email: severin@gsc.riken.jp

Alternatively, for more information please contact:

Juliette Savin
Global Relations Office
RIKEN
Tel: +81-(0)48-462-1225
Email: pr@riken.jp

A copy of the original Nature Biotechnology article and a figure are available on request.

Reference

  • Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, the FANTOM consortium, Nicolas Bertin, and Alistair RR Forrest. "Interactive visualization and analysis of large-scale NGS data-sets using ZENBU". Nature Biotechnology, http://dx.doi.org/10.1038/nbt.2840 (2013)

     

About RIKEN

RIKEN is Japan's flagship research institute for basic and applied research. Over 2500 papers by RIKEN researchers are published every year in reputable scientific and technical journals, covering topics ranging across a broad spectrum of disciplines including physics, chemistry, biology, medical science and engineering. RIKEN's advanced research environment and strong emphasis on interdisciplinary collaboration has earned itself an unparalleled reputation for scientific excellence in Japan and around the world.

Website: http://www.riken.jp Find us on Twitter at @riken_en

About the Center for Life Science Technologies (CLST) The RIKEN Center for Life Science Technologies aims at the development of key technologies for breakthroughs in medical and pharmaceutical applications by conducting ground-breaking research and development programs for next-generation life sciences. CLST comprises the Division of Structural and Synthetic Biology, the Division of Genomic Technologies, and the Division of Bio-function Dynamics Imaging, which will work together in this endeavor. Research and development programs are carried out in collaboration with companies, universities, and international consortia, in order to disseminate the center's achievements to the global community.

Website: http://www.clst.riken.jp/en/index.html

Juliette Savin | EurekAlert!

Further reports about: Accelerator Analysis Biotechnology CAGE Division Genome RIKEN RNA-seq difference experiments mechanisms

More articles from Life Sciences:

nachricht Algorithms Offer Insight into Cellular Development
31.08.2016 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt

nachricht Cancer: Molecularly shutting down cancer cachexia
31.08.2016 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Virtual Reality: 3D Human Body Reconstruction from Fraunhofer HHI digitizes Human Beings

Scientists at the Fraunhofer Institute for Telecommunications, Heinrich Hertz Institute, HHI have developed a method by which the realistic image of a person can be transmitted into a virtual world. The 3D Human Body Reconstruction Technology captures real persons with multiple cameras at the same time and creates naturally moving dynamic 3D models. At this year’s trade fairs IFA in Berlin (Hall 11.1, Booth 3) and IBC in Amsterdam (Hall 8, Booth B80) Fraunhofer HHI will show this new technology.

Fraunhofer HHI researchers have developed a camera system that films people with a perfect three-dimensional impression. The core of this system is a stereo...

Im Focus: Streamlining accelerated computing for industry

PyFR code combines high accuracy with flexibility to resolve unsteady turbulence problems

Scientists and engineers striving to create the next machine-age marvel--whether it be a more aerodynamic rocket, a faster race car, or a higher-efficiency jet...

Im Focus: X-ray optics on a chip

Waveguides are widely used for filtering, confining, guiding, coupling or splitting beams of visible light. However, creating waveguides that could do the same for X-rays has posed tremendous challenges in fabrication, so they are still only in an early stage of development.

In the latest issue of Acta Crystallographica Section A: Foundations and Advances , Sarah Hoffmann-Urlaub and Tim Salditt report the fabrication and testing of...

Im Focus: Piggyback battery for microchips: TU Graz researchers develop new battery concept

Electrochemists at TU Graz have managed to use monocrystalline semiconductor silicon as an active storage electrode in lithium batteries. This enables an integrated power supply to be made for microchips with a rechargeable battery.

Small electrical gadgets, such as mobile phones, tablets or notebooks, are indispensable accompaniments of everyday life. Integrated circuits in the interiors...

Im Focus: UCI physicists confirm possible discovery of fifth force of nature

Light particle could be key to understanding dark matter in universe

Recent findings indicating the possible discovery of a previously unknown subatomic particle may be evidence of a fifth fundamental force of nature, according...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

The energy transition is not possible without Geotechnics

25.08.2016 | Event News

New Ideas for the Shipping Industry

24.08.2016 | Event News

A week of excellence: 22 of the world’s best computer scientists and mathematicians in Heidelberg

12.08.2016 | Event News

 
Latest News

Cancer: Molecularly shutting down cancer cachexia

31.08.2016 | Life Sciences

Robust fuel cell heating unit developed

31.08.2016 | Power and Electrical Engineering

Algorithms Offer Insight into Cellular Development

31.08.2016 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>