Navigation Links
UMD researchers develop tool to better visualize, analyze human genomic data
Date:8/3/2014

Scientists at the University of Maryland have developed a new, web-based tool that enables researchers to quickly and easily visualize and compare large amounts of genomic information resulting from high-throughput sequencing experiments. The free tool, called Epiviz, was described in a paper published online on August 3, 2014 in the journal Nature Methods.

Next-generation sequencing has revolutionized functional genomics. These techniques are key to understanding the molecular mechanisms underlying cell function in healthy and diseased individuals and the development of diseases like cancer. Data from multiple experiments need to be integrated, but the growing number of data sets makes a thorough comparison and analysis of results challenging.

To visualize and browse entire genomes, graphical interfaces that display information from a database of genomic datacalled "genome browsers"were created. Epiviz offers a major advantage over browsers currently available: Epiviz seamlessly integrates with the open-source Bioconductor analysis software widely used by genomic scientists, through its Epivizr Bioconductor package.

"Prior tools limited visualization to presentation and dissemination, rather than a hybrid tool integrating interactive visualization with algorithmic analysis," says Hctor Corrada Bravo, assistant professor in computer science at UMD. He also has an appointment in the Center for Bioinformatics and Computational Biology of the university's Institute for Advanced Computer Studies.

Because Epiviz is based on the Bioconductor infrastructure, the tool supports many popular next-generation sequencing techniques, such as ChIP-seq, which is used to analyze protein interactions with DNA; RNA-seq, which reveals a comprehensive snapshot of the abundance of RNAs in cells; and DNA methylation analyses.

Epiviz implements multiple visualization methods for location-based data (such as genomic regions of interest) and feature-based data (such as gene expression), using interactive data visualization techniques not available in web-based genome browsers. For example, because display objects are mapped directly to data elements, Epiviz links data across different visualizations giving users visual insights of the spatial relationships of multiple data sets. The tool is designed to allow biomedical scientists to easily incorporate their own visualizations.

In the Nature Methods paper, Corrada Bravo, UMD computer science doctoral student Florin Chelaru, and undergraduate research assistants from Williams College in Mass. and Washington University in St. Louis used Epiviz to visualize and analyze DNA methylation and gene expression data in colon cancer. Changes in DNA methylation patterns compared with normal tissue have been associated with a large number of human malignancies.

Using Epiviz and Bioconductor, the research team found consistent regions of DNA methylation changes in colon cancer samples generated by the public Cancer Genome Atlas project and similar gene expression in these regions of DNA methylation changes in other cancer types. The results were in agreement with previous experiments, which were conducted by researchers at Johns Hopkins University in collaboration with Corrada Bravo, showing DNA methylation changes across large regions in the colon cancer genome.

"Epiviz helps biomedical scientists meet the challenge of visualizing large genomic data sets while supporting creative data analysis in a collaborative environment," says Corrada Bravo.


'/>"/>

Contact: Abby Robinson
abbyr@umd.edu
301-405-5845
University of Maryland
Source:Eurekalert  

Related biology news :

1. New method provides researchers with efficient tool for tagging proteins
2. Researchers uncover secrets of internal cell fine-tuning
3. Whitehead Institute researchers create naïve pluripotent human embryonic stem cells
4. UNC researchers find unsuspected characteristics of new CF drugs, offering potential paths to more effective therapies
5. York University researchers use bird backpacks to put wood thrushes migration on the map
6. Intestinal parasites are old friends, researchers argue
7. UNH NHAES researchers work to save endangered New England cottontail
8. Researchers create vaccine for dust-mite allergies
9. Cleveland Clinic researchers discover neuroprotective role of immune cell
10. Researchers provide guide to household water conservation
11. UCI researchers find epigenetic tie to neuropsychiatric disorders
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
UMD researchers develop tool to better visualize, analyze human genomic data
(Date:5/12/2016)... 2016 WearablesResearch.com , a brand of ... results from the Q1 wave of its quarterly wearables ... consumers, receptivity to a program where they would receive ... insurance company. "We were surprised to see ... Michael LaColla , CEO of Troubadour Research, "primarily because ...
(Date:4/28/2016)... , April 28, 2016 Infosys ... (NYSE: INFY ), and Samsung SDS, a global ... that will provide end customers with a more secure, fast ...      (Logo: http://photos.prnewswire.com/prnh/20130122/589162 ) , ... but it also plays a fundamental part in enabling and ...
(Date:4/26/2016)... -- Research and Markets has announced the ...  report to their offering.  , ,     (Logo: ... forecast the global multimodal biometrics market to grow ... 2016-2020.  Multimodal biometrics is being implemented ... healthcare, BFSI, transportation, automotive, and government for controlling ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... , ... June 27, 2016 , ... ... bring innovative medical technologies, services and solutions to the healthcare market. The company's ... of various distribution, manufacturing, sales and marketing strategies that are necessary to help ...
(Date:6/27/2016)... 2016  Liquid Biotech USA ... a Sponsored Research Agreement with The University of ... from cancer patients.  The funding will be used ... with clinical outcomes in cancer patients undergoing a ... be employed to support the design of a ...
(Date:6/24/2016)... on a range of subjects including policies, debt and investment ... Speaking at a lecture to the Canadian Economics ... the country,s inflation target, which is set by both the ... "In certain areas there needs to be frequent ... not sit down and address strategy together?" He ...
(Date:6/24/2016)... ... June 24, 2016 , ... While the majority of commercial ... Cary 5000 and the 6000i models are higher end machines that use the more ... the spectrophotometer’s light beam from the bottom of the cuvette holder. , FireflySci ...
Breaking Biology Technology: