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Journal of Clinical Bioinformatics

, 4:5

First Online: 31 March 2014Received: 23 December 2013Accepted: 26 March 2014DOI: 10.1186-2043-9113-4-5

Cite this article as: Mader, M., Simon, R. & Kurtz, S. J Clin Bioinform 2014 4: 5. doi:10.1186-2043-9113-4-5

Abstract

BackgroundA 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.

ResultsWe 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.

ConclusionsThe 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 at http:-www.zbh.uni-hamburg.de-fishoracle.

KeywordsGenomic data Integrative visualization Cancer genomics Web server GenomeTools ICGC TCGA TTC28 Electronic supplementary materialThe online version of this article doi:10.1186-2043-9113-4-5 contains supplementary material, which is available to authorized users.

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Autor: Malte Mader - Ronald Simon - Stefan Kurtz

Fuente: https://link.springer.com/







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