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 data—called "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 Héctor 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.
This research was supported by the National Institutes of Health (Award Nos. HG006102 and HG005220), Illumina Corp. and Genentech. The content of this article does not necessarily reflect the views of these organizations.
Héctor Corrada Bravo website: http://www.cbcb.umd.edu/~hcorrada/
The research paper, "Epiviz: interactive visual analytics for functional genomics data," Florin Chelaru, Llewellyn Smith, Naomi Goldstein and Héctor Corrada Bravo, was published online Aug. 3, 2014 in Nature Methods. http://dx.doi.org/10.1038/nmeth.3038
Media Relations Contact: Abby Robinson, 301-405-5845, email@example.com
University of Maryland
College of Computer, Mathematical, and Natural Sciences
2300 Symons Hall
College Park, Md. 20742
About the College of Computer, Mathematical, and Natural Sciences
The College of Computer, Mathematical, and Natural Sciences at the University of Maryland educates more than 7,000 future scientific leaders in its undergraduate and graduate programs each year. The college's 10 departments and more than a dozen interdisciplinary research centers foster scientific discovery with annual sponsored research funding exceeding $150 million.
Abby Robinson | Eurek Alert!
Researchers develop eco-friendly, 4-in-1 catalyst
25.04.2017 | Brown University
Transfecting cells gently – the LZH presents a GNOME prototype at the Labvolution 2017
25.04.2017 | Laser Zentrum Hannover e.V.
More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.
Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...
Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.
"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...
The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.
Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...
The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...
Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.
Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...
20.04.2017 | Event News
18.04.2017 | Event News
03.04.2017 | Event News
25.04.2017 | Physics and Astronomy
25.04.2017 | Materials Sciences
25.04.2017 | Life Sciences