Dataset Information

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

ABSTRACT: 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 at http://www.zbh.uni-hamburg.de/fishoracle.

SUBMITTER: Mader M

PROVIDER: S-EPMC4230720 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Publications

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

Mader Malte M Simon Ronald R Kurtz Stefan S

Journal of clinical bioinformatics 20140331 1

<h4>Background</h4>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.<h4>Results</h4>We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data ty ...[more]

PMID: 24684958

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Project description:BackgroundNext-generation sequencing (NGS) has been widely used in both clinics and research. It has become the most powerful tool for diagnosing genetic disorders and investigating disease etiology through the discovery of genetic variants. Variants identified by NGS are stored in variant call format (VCF) files. However, querying and filtering VCF files are extremely difficult for researchers without programming skills. Furthermore, as the mutation data are increasing exponentially, there is an urgent need to develop tools to manage these variant data in a centralized way.MethodsThe VCF-Server was developed as a web-based visualization tool to support the interactive analysis of genetic variant data. It allows researchers and medical geneticists to manage, annotate, filter, query, and export variants in a fast and effective way.ResultsIn this study, we developed the VCF-Server, a powerful and easily accessible tool for researchers and medical geneticists to perform variant analysis. Users can query VCFs, annotate, and filter variants without knowing programming code. Once the VCF file is uploaded, VCF-Server allows users to annotate the VCF with commonly used databases or user-defined variant annotations (including variant blacklist and whitelist). Variant information in the VCF is shown visually via the interactive graphical interface. Users can filter the variants with flexible filtering rules, and the prioritized variants can be exported locally for further analysis. As VCF-Server adopts a web file system, files in the VCF-Server can be stored and managed in a centralized way. Moreover, VCF-Server allows direct web-based analysis (accessible through either desktop computers or mobile devices) as well as local deployment.ConclusionsWith an easy-to-use graphical interface, VCF-Server allows researchers with little bioinformatics background to explore and mine mutation data, which may broaden the application of NGS technology in clinics and research. The tool is freely available for use at https://www.diseasegps.org/VCF-Server?lan = eng.

Dataset Information

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

Publications

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

Similar Datasets

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