We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
INTEGRA BIOSCIENCES AG

Download Mobile App




Visualizing Transcriptomes with New Bioinformatics Application

By LabMedica International staff writers
Posted on 19 Mar 2014
Print article
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


Platinum Member
COVID-19 Rapid Test
OSOM COVID-19 Antigen Rapid Test
HLX
Anti-Cyclic Citrullinated Peptide Test
GPP-100 Anti-CCP Kit
Gold Member
Real-time PCR System
GentierX3 Series

Print article

Channels

Clinical Chemistry

view channel
Image: Reaching speeds up to 6,000 RPM, this centrifuge forms the basis for a new type of inexpensive, POC biomedical test (Photo courtesy of Duke University)

POC Biomedical Test Spins Water Droplet Using Sound Waves for Cancer Detection

Exosomes, tiny cellular bioparticles carrying a specific set of proteins, lipids, and genetic materials, play a crucial role in cell communication and hold promise for non-invasive diagnostics.... Read more

Molecular Diagnostics

view channel
Image: The study showed the blood-based cancer screening test detects 83% of people with colorectal cancer with specificity of 90% (Photo courtesy of Guardant Health)

Blood Test Shows 83% Accuracy for Detecting Colorectal Cancer

Colorectal cancer is the second biggest cause of cancer deaths among adults in the U.S., with forecasts suggesting 53,010 people might die from it in 2024. While fewer older adults are dying from this... Read more

Hematology

view channel
Image: The Gazelle Hb Variant Test (Photo courtesy of Hemex Health)

First Affordable and Rapid Test for Beta Thalassemia Demonstrates 99% Diagnostic Accuracy

Hemoglobin disorders rank as some of the most prevalent monogenic diseases globally. Among various hemoglobin disorders, beta thalassemia, a hereditary blood disorder, affects about 1.5% of the world's... Read more

Microbiology

view channel
Image: The new platform is designed to perform blood-based diagnoses of nontuberculosis mycobacteria (Photo courtesy of 123RF)

New Blood Test Cuts Diagnosis Time for Nontuberculous Mycobacteria Infections from Months to Hours

Breathing in nontuberculous mycobacteria (NTM) is a common experience for many people. These bacteria are present in water systems, soil, and dust all over the world and usually don't cause any problems.... Read more

Industry

view channel
Image: These new assays are being developed for use on the recently introduced DxI 9000 Immunoassay Analyzer (Photo courtesy of Beckman Coulter)

Beckman Coulter and Fujirebio Expand Partnership on Neurodegenerative Disease Diagnostics

Beckman Coulter Diagnostics (Brea, CA, USA) and Fujirebio Diagnostics (Tokyo, Japan) have expanded their partnership focused on the development, manufacturing and clinical adoption of neurodegenerative... Read more
Copyright © 2000-2024 Globetech Media. All rights reserved.