FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research

Journal of Clinical Bioinformatics

Stefan Kurtz²  Ronald Simon¹  Malte Mader¹ 

[1] Department of Pathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany;Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany

关键词: TTC28;    TCGA;    ICGC;    GenomeTools;    Web server;    Cancer genomics;    Integrative visualization;    Genomic data;   

Others  :  800992
DOI  :  10.1186/2043-9113-4-5

 received in 2013-12-23, accepted in 2014-03-26,  发布年份 2014

【 摘 要 】

Background

A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events.

Results

We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before.

Conclusions

The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available athttp://www.zbh.uni-hamburg.de/fishoracle webcite.

【 授权许可】

   
2014 Mader et al.; licensee BioMed Central Ltd.

【 图 表 】

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