New web based tool allows researchers to quickly visualize genomic information -
Scientists from the University of Maryland have developed a new tool based on the Web that allows researchers to quickly and easily view and compare large amounts of genomic data from high-throughput sequencing experiments. The free tool, called Epiviz, was described in an article published online August 3, 2014 review Nature Methods .
functional genomicsNext-generation sequencing has revolutionized. These techniques are essential to understand the underlying molecular mechanisms of cell function in healthy individuals and patients and the development of diseases like cancer. Data from multiple experiments to be integrated, but the increasing number of datasets made a comparison and analysis of results difficult to cross.
To view and browse entire genomes, graphical interfaces that display information from a genomic database data -called "genome browsers" -were created. Epiviz offers a major advantage over the currently available browsers :. Epiviz integrates seamlessly with the open-source Bioconductor analysis software widely used by researchers in genomics, through its packaging Epivizr Bioconductor
"previous tools limited viewing the presentation and dissemination, rather a hybrid incorporating interactive visualization tool with the algorithmic analysis, "said H-ctor Corrada Bravo, assistant professor of computer science at UMD. It also has an appointment in the Bioinformatics and Computational Biology Center of the Institute of the University of Computer Studies higher.
Because Epiviz Bioconductor is based on the infrastructure, the tool supports many popular next generation sequencing techniques, such as ChIP-seq, which is used to analyze protein interactions with the DNA; RNA-seq, which reveals a complete overview of the abundance of RNA in the cells; and DNA methylation analysis.
Epiviz implements several methods of geolocation data visualization (such as genomic regions of interest) and data based features (such as gene expression), using visualization techniques interactive data is not available in web browsers based genome. For example, because display objects are mapped directly to the data elements, Epiviz links data across different visualizations giving users a visual spatial relationships of multiple data sets. The tool is designed to enable biomedical scientists to easily integrate their own visualizations.
Within Nature Methods paper, Corrada Bravo, PhD Florin Chelaru computer UMD, and research assistants first cycle of Williams College in Mass. and Washington University in St. Louis Epiviz used to visualize and analyze DNA methylation data and gene expression in colon cancer. Changes in the DNA methylation patterns compared to normal tissue have been associated with many human malignancies.
Using Epiviz and Bioconductor, the research team found coherent regions of DNA methylation changes in colon cancer samples generated by the Cancer Genome Atlas project and public gene expression similar in these regions DNA methylation changes in other types of cancer. The results are consistent with previous experiments, which were conducted by researchers from Johns Hopkins University, in collaboration with Corrada Bravo, showing DNA methylation changes in large areas in the genome of colon cancer.
"Epiviz help biomedical scientists meet the challenge to visualize large sets of genomic data, while supporting the analysis of the creation of data in a collaborative environment," said Corrada Congratulations.
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