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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



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