Featured Research

from universities, journals, and other organizations

Next Generation Tool For Visualizing Genomic Data Introduced

Date:
August 6, 2008
Source:
Broad Institute of MIT and Harvard
Summary:
Researchers are collecting vast amounts of genomic data, but ways to visualize these data in an integrated manner have lagged behind the ability to generate them. Researchers have now developed a novel and freely available visualization tool that helps users integrate and analyze different types of genomic data, and gives them the flexibility to zoom in on a specific region of interest or to pan out for a broad, whole genome view.

A genome-wide view of DNA copy number variations in patients with a form of brain cancer.
Credit: Image courtesy of Wendy Winckler, Broad Institute

Researchers are collecting vast amounts of diverse genomic data with ever-increasing speed, but effective ways to visualize these data in an integrated manner have lagged behind the ability to generate them.

To address this growing need, researchers at the Broad Institute have developed the Integrative Genomics Viewer (IGV), a novel and freely available visualization tool that helps users simultaneously integrate and analyze different types of genomic data, and gives them the flexibility to zoom in on a specific genomic region of interest or to pan out for a broad, whole genome view.

"This new tool offers a Google Maps-like view of integrative genomic data," said Jill Mesirov, Chief Informatics Officer and Director of Computational Biology and Bioinformatics at the Broad Institute. "It brings together different kinds of genomic data into a single, holistic view. I'm incredibly proud of our computational scientists for responding so rapidly and effectively to the critical needs of the growing genomics research community."

With IGV, researchers can still choose a Google Maps-like "street view" of the As, Cs, Ts, and Gs that make up the genome, but they can also simultaneously visualize additional layers of complex information about gene expression as well as sequence alterations, or mutations, in the genetic code. Other genomic details, such as copy number variation, chromatin immunoprecipation data, and epigenetic modifications, can also be viewed in IGV. Moreover, all these data types can be overlaid or superimposed to determine how changes at one level will affect another. Users can choose from a variety of display options, viewing their data as a heat map, histogram, scatter plot, or other formats of their choice. This new visualization tool is free and publicly available to researchers via the web.

"Other tools offer detailed, localized views of genomic data, and a few tools are equipped to provide a whole genome view," said Senior Software Engineer Jim Robinson, one of the program's creators. "IGV was designed to integrate both and to provide smooth zooming and panning across all resolution scales. "

"Most visualization tools are limited in their ability to handle multiple types of genomic data and are typically 'retrofitted' to accommodate new data types as they have arisen," said Michael Reich, Director of Cancer Informatics Development at the Broad Institute. "IGV was designed from the ground up to integrate all of these data, and to provide a strong platform for future growth and refinement."

Broad Associate Member John Rinn, an assistant professor at Harvard University and Beth Israel Deaconess Medical Center, has used a variety of visualization tools to sift through different types of genomic data. "Before I was introduced to IGV, I had to use three different programs to visually integrate my data," Rinn said. "But now this one, universal browser allows me to rapidly scan the entire genome and identify promising regions, which has revolutionized my work."

IGV promises to increase the flow of discovery in many areas of biomedical research. "This tool is designed to enable researchers to view many types of genomic data, especially those relevant to human disease," said Reich. "We're particularly excited about its already groundbreaking use in ongoing studies of the cancer genome."

IGV is made publicly available to researchers worldwide and can be accessed at: http://www.broad.mit.edu/igv


Story Source:

The above story is based on materials provided by Broad Institute of MIT and Harvard. Note: Materials may be edited for content and length.


Cite This Page:

Broad Institute of MIT and Harvard. "Next Generation Tool For Visualizing Genomic Data Introduced." ScienceDaily. ScienceDaily, 6 August 2008. <www.sciencedaily.com/releases/2008/08/080804111644.htm>.
Broad Institute of MIT and Harvard. (2008, August 6). Next Generation Tool For Visualizing Genomic Data Introduced. ScienceDaily. Retrieved September 14, 2014 from www.sciencedaily.com/releases/2008/08/080804111644.htm
Broad Institute of MIT and Harvard. "Next Generation Tool For Visualizing Genomic Data Introduced." ScienceDaily. www.sciencedaily.com/releases/2008/08/080804111644.htm (accessed September 14, 2014).

Share This



More Plants & Animals News

Sunday, September 14, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Conservationists Face Uphill PR Battle With New Shark Rules

Conservationists Face Uphill PR Battle With New Shark Rules

Newsy (Sep. 14, 2014) — New conservation measures for shark fishing face an uphill PR battle in the fight to slow shark extinction. Video provided by Newsy
Powered by NewsLook.com
Shocker: Journalists Are Utterly Addicted To Coffee

Shocker: Journalists Are Utterly Addicted To Coffee

Newsy (Sep. 13, 2014) — A U.K. survey found that journalists consumed the most amount of coffee, but that's only the tip of the coffee-related statistics iceberg. Video provided by Newsy
Powered by NewsLook.com
'Magic Mushrooms' Could Help Smokers Quit

'Magic Mushrooms' Could Help Smokers Quit

Newsy (Sep. 11, 2014) — In a small study, researchers found that the majority of long-time smokers quit after taking psilocybin pills and undergoing therapy sessions. Video provided by Newsy
Powered by NewsLook.com
Spinosaurus Could Be First Semi-Aquatic Dinosaur

Spinosaurus Could Be First Semi-Aquatic Dinosaur

Newsy (Sep. 11, 2014) — New research has shown that the Spinosaurus, the largest carnivorous dinosaur, might have been just as well suited for life in the water as on land. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

    Technology News



    Save/Print:
    Share:  

    Free Subscriptions


    Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

    Get Social & Mobile


    Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

    Have Feedback?


    Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
    Mobile iPhone Android Web
    Follow Facebook Twitter Google+
    Subscribe RSS Feeds Email Newsletters
    Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins