Features | Partner Sites | Information | LinkXpress
Sign In
JIB
GLOBETECH PUBLISHING
BioConferenceLive

Visualizing Transcriptomes with New Bioinformatics Application

By BiotechDaily International staff writers
Posted on 19 Mar 2014
Image: Overview of the ZENBU genome browser interface showcasing several on-demand processing tracks for selected ENCODE datasets (experiment involving Gm12878, Hela and Nhek cell lines) (Photo courtesy of the RIKEN Center for Life Science Technology).
Image: Overview of the ZENBU genome browser interface showcasing several on-demand processing tracks for selected ENCODE datasets (experiment involving Gm12878, Hela and Nhek cell lines) (Photo courtesy of the RIKEN Center for Life Science Technology).
A new, freely available bioinformatics application enables scientists to rapidly and easily visualize, integrate, and compare large amounts of genomic data resulting from large-scale, next-generation sequencing research.

The new tool, called ZENBU, was developed at the RIKEN Center for Life Science Technology (Kobe, Japan), The new tool will allow researchers to rapidly and easily incorporate, 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 (RNA sequencing), ChIP-seq (chromatin immunoprecipitation), and CAGE (cap analysis of gene expression) being employed widely worldwide. The efficacy of these techniques lies in the fact that they enable the genome-wide discovery of transcripts and transcription factor-binding sites, which is crucial to better understanding the molecular processing underlying cell function in healthy and diseased individuals and the development of diseases such as cancer. The integration of data from multiple research efforts is an important feature of the interpretation of findings; however, the growing number of datasets generated makes a thorough comparison and analysis of findings unwieldy.

In a report published March 9, 2014, in the journal Nature Biotechnology, Dr. Jessica Severin and colleagues described 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 earlier developed tools is the ability to dynamically combine thousands of research datasets in an interactive visualization setting through linked genome location and expression signal views. This allows scientists to compare their own research against the over 6,000 ENCODE and FANTOM consortium datasets currently loaded into the system, thereby enabling them to discover new and noteworthy biologic processes. The tool is designed to incorporate millions of experiments/datasets of any kind (RNA-seq, ChIP-seq or CAGE), hence, its name: zenbu means in Japanese “all” or “everything.”

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 online (Please see Related Links below).

“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,” explained the researchers.

Related Links:

RIKEN Center for Life Science Technology
Zenbu Transcriptomes Dataset Tool



comments powered by Disqus

Channels

Genomics/Proteomics

view channel
Image: Blocking the activity of HSP101 may imprison the malaria parasite inside its protective vacuole within the red blood cell. In the electron micrograph, the malaria parasites appear in blue and uninfected red blood cells are shown in red (Photo courtesy of the [US] National Institute of Allergy and Infectious Diseases).

Heat Shock Protein Plays Critical Role in Malaria Parasite Protein Trafficking

A pair of recent papers described the molecular operators that enable the malaria parasite Plasmodium falciparum to export a large variety of proteins across the parasitophorous vacuolar membrane (PVM)... Read more

Drug Discovery

view channel
Image: Molecular rendering of the crystal structure of parkin (Photo courtesy of Wikimedia Commons).

Cinnamon Feeding Blocks Development of Parkinson's Disease in Mouse Model

A team of neurological researchers has identified a molecular mechanism by which cinnamon acts to protect neurons from damage caused by Parkinson's disease (PD) in a mouse model of the syndrome.... Read more

Therapeutics

view channel
Image: This type of electronic pacemaker could become obsolete if induction of biological pacemaker cells by gene therapy proves successful (Photo courtesy of Wikimedia Commons).

Gene Therapy Induces Functional Pacemaker Cells in Pig Heart Failure Model

Cardiovascular disease researchers working with a porcine heart failure model have demonstrated the practicality of using gene therapy to replace implanted electronic pacemakers to regulate heartbeat.... Read more

Business

view channel

Cancer Immunotherapy Sector Predicted to Surge to USD 9 Billion Across Major Pharma Through 2022

The immunotherapy market will experience substantial growth through 2022, increasing from USD 1.1 billion in 2012 to nearly USD 9 billion in 2022 (corresponding to 23.8% annual growth) in the United Kingdom, United States, France, Germany, Italy, Spain, and Japan, according to recent market research. This notable growth... Read more
 
Copyright © 2000-2014 Globetech Media. All rights reserved.