Featured Research

from universities, journals, and other organizations

New bioinformatics tool to visualize transcriptomes

Date:
March 9, 2014
Source:
RIKEN
Summary:
ZENBU, a new, freely available bioinformatics tool 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.

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.


Story Source:

The above story is based on materials provided by RIKEN. Note: Materials may be edited for content and length.


Journal Reference:

  1. 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, March 2014 DOI: 10.1038/nbt.2840

Cite This Page:

RIKEN. "New bioinformatics tool to visualize transcriptomes." ScienceDaily. ScienceDaily, 9 March 2014. <www.sciencedaily.com/releases/2014/03/140309150538.htm>.
RIKEN. (2014, March 9). New bioinformatics tool to visualize transcriptomes. ScienceDaily. Retrieved July 24, 2014 from www.sciencedaily.com/releases/2014/03/140309150538.htm
RIKEN. "New bioinformatics tool to visualize transcriptomes." ScienceDaily. www.sciencedaily.com/releases/2014/03/140309150538.htm (accessed July 24, 2014).

Share This




More Computers & Math News

Thursday, July 24, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Robot Parking Valet Creates Stress-Free Travel

Robot Parking Valet Creates Stress-Free Travel

AP (July 23, 2014) 'Ray' the robotic parking valet at Dusseldorf Airport in Germany lets travelers to avoid the hassle of finding a parking spot before heading to the check-in desk. (July 23) Video provided by AP
Powered by NewsLook.com
Six Indicted in StubHub Hacking Scheme

Six Indicted in StubHub Hacking Scheme

AP (July 23, 2014) Six people were indicted Wednesday in an international ring that took over more than 1,000 StubHub users' accounts and fraudulently bought tickets that were then resold. (July 23) Video provided by AP
Powered by NewsLook.com
The Reviews Are In For The Amazon Fire Phone

The Reviews Are In For The Amazon Fire Phone

Newsy (July 23, 2014) Amazon's first smartphone, the Fire Phone, is set to ship this week, and so far the reviews have been pretty mixed. Video provided by Newsy
Powered by NewsLook.com
Bigger Apple Phone, Bigger Orders

Bigger Apple Phone, Bigger Orders

Reuters - Business Video Online (July 22, 2014) Apple is asking suppliers to make 70 to 80 million units of its new larger screen iPhone, a lot more initially than its current model. Fred Katayama reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins