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 29, 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 29, 2014).

Share This




More Computers & Math News

Tuesday, July 29, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Teen's Phone Ignites Under Her Pillow; How Real Is The Risk?

Teen's Phone Ignites Under Her Pillow; How Real Is The Risk?

Newsy (July 28, 2014) A Texas teen's Samsung phone apparently ignited while she slept, but what was the real problem here? Video provided by Newsy
Powered by NewsLook.com
Google's Next Frontier: The Human Body

Google's Next Frontier: The Human Body

Newsy (July 27, 2014) Google is collecting genetic and molecular information to paint a picture of the perfectly healthy human. Video provided by Newsy
Powered by NewsLook.com
Cellphone Unlocking Bill Clears U.S. House, Heads to Obama

Cellphone Unlocking Bill Clears U.S. House, Heads to Obama

Reuters - US Online Video (July 27, 2014) Congress gets rid of pesky law that made it illegal to "unlock" mobile phones without permission, giving consumers the option to use the same phone on a competitor's wireless network. Mana Rabiee reports. Video provided by Reuters
Powered by NewsLook.com
Congress OKs Unlocking Phones From Carriers

Congress OKs Unlocking Phones From Carriers

Newsy (July 26, 2014) A bill legalizing "unlocking," or untethering a phone from its default wireless carrier, has passed Congress and is expected to be signed into law. Video provided by Newsy
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