Featured Research

from universities, journals, and other organizations

Computational feat speeds finding of genes to milliseconds instead of years

Date:
March 16, 2010
Source:
Stanford University Medical Center
Summary:
Like a magician who says, "Pick a card, any card," computer scientist Debashis Sahoo seemed to be offering some kind of trick when he asked researchers to pick any two genes already known to be involved in stem cell development. Finding such genes can take years and hundreds of thousands of dollars, but Sahoo was promising the skeptical stem cell scientists that, in a fraction of a second and for practically zero cost, he could find new genes involved in the same developmental pathway as the two genes provided. Sahoo went on to show that this amazing feat could actually be performed.

Like a magician who says, "Pick a card, any card," Stanford University computer scientist Debashis Sahoo, PhD, seemed to be offering some kind of trick when he asked researchers at the Stanford Institute for Stem Cell Biology and Regenerative Medicine to pick any two genes already known to be involved in stem cell development. Finding such genes can take years and hundreds of thousands of dollars, but Sahoo was promising the skeptical stem cell scientists that, in a fraction of a second and for practically zero cost, he could find new genes involved in the same developmental pathway as the two genes provided.

Sahoo went on to show that this amazing feat could actually be performed. The proof-of-principle for his idea, to be published online March 15 in the Proceedings of the National Academy of Sciences, opens a powerful, mathematical route for conducting stem cell research and shows the power of interdisciplinary collaborations in science. It also demonstrates that using computers to mine existing databases can radically accelerate research in the laboratory. Ultimately, it may lead to advances in diverse areas of medicine such as disease diagnosis or cancer therapy.

Biologists have long used math and statistics in their work. In the simplest case, when looking for genes involved in a certain biological process, they look for genes that have a symmetrical correlation. For instance, if they know gene A is involved in a certain process, they try to determine if gene C is correlated with gene A during the same process.

Four years ago, while studying for his doctorate in electrical engineering with advisor David Dill, PhD, professor of computer science, and co-advisor Sylvia Plevritis, PhD, associate professor of radiology, Sahoo took an immunology class and realized that many of the relationships in biology are not symmetric, but asymmetric. As an analogy, Sahoo noted that trees bearing fruit almost certainly have leaves, but trees outside of the fruiting season may or may not have leaves, depending on the time of year.

Sahoo and Dill realized that these asymmetric relationships could be found by applying Boolean logic, in which the researchers established a series of if/then rules and then searched data for candidates that satisfied all the rules. For example, scientists might know that gene A is very active at the beginning of cell development, and gene C is active much later. By screening large public databases, Sahoo can find the genes that are almost never active when A is active, and almost always active when C is active, in many other types of cells. Researchers can then test to determine whether these genes become active between the early and late stages of development.

In the paper, lead author Sahoo looked at gene expression patterns in the development of an immunological cell called a B cell. Starting with two known B-cell genes, Sahoo searched through databases with thousands of gene products in milliseconds and found 62 genes that matched the patterns he would expect to see for genes that got turned on in between the activation of the two genes he started with. He then examined databases involving 41 strains of laboratory mice that had been engineered to be deficient in one or more of the 62 genes. Of those 41 strains, 26 had defects in B cell development.

"This was the validation of the method," Sahoo said. "Biologists are really amazed that, with just a computer algorithm, in milliseconds I can find genes that it takes them a really long time to isolate in the lab." He added that he was especially gratified that the information comes from databases that are widely available and from which other scientists have already culled information.

Sahoo is now using the technique to find new genes that play a role in developing cancers.

"This shows that computational analysis of existing data can provide clues about where researchers should look next," he said. "This is something that could have an impact on cancer. It's exciting."

The interdisciplinary team that contributed to the findings involved researchers at both the School of Engineering and the School of Medicine. In addition to Dill (the paper's senior author) and Plevritis, the co-authors include Irving Weissman, MD, director of Stanford's stem cell institute, and postdoctoral scholars Jun Seita, PhD, Matthew Inlay, PhD, and Deepta Bhattacharya, PhD, who recently moved from Stanford to the Washington University School of Medicine in St. Louis.

Funding for this research came from the National Institutes of Health, the Siebel Stem Cell Institute, the Thomas and Stacey Siebel Foundation, the Cancer Research Institute, the National Cancer Institute and the California Institute for Regenerative Medicine.


Story Source:

The above story is based on materials provided by Stanford University Medical Center. The original article was written by Christopher Vaughan, Communications officer, Stanford Institute for Stem Cell Biology and Regenerative Medicine. Note: Materials may be edited for content and length.


Journal Reference:

  1. Debashis Sahoo, Jun Seita, Deepta Bhattacharya, Matthew A. Inlay, Irving L. Weissman, Sylvia K. Plevritis, and David L. Dill. MiDReG: A method of mining developmentally regulated genes using Boolean implications. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.0913635107

Cite This Page:

Stanford University Medical Center. "Computational feat speeds finding of genes to milliseconds instead of years." ScienceDaily. ScienceDaily, 16 March 2010. <www.sciencedaily.com/releases/2010/03/100315161915.htm>.
Stanford University Medical Center. (2010, March 16). Computational feat speeds finding of genes to milliseconds instead of years. ScienceDaily. Retrieved August 1, 2014 from www.sciencedaily.com/releases/2010/03/100315161915.htm
Stanford University Medical Center. "Computational feat speeds finding of genes to milliseconds instead of years." ScienceDaily. www.sciencedaily.com/releases/2010/03/100315161915.htm (accessed August 1, 2014).

Share This




More Plants & Animals News

Friday, August 1, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Ebola Vaccine Might Be Coming, But Where's It Been?

Ebola Vaccine Might Be Coming, But Where's It Been?

Newsy (Aug. 1, 2014) Health officials are working to fast-track a vaccine — the West-African Ebola outbreak has killed more than 700. But why didn't we already have one? Video provided by Newsy
Powered by NewsLook.com
Study Links Certain Birth Control Pills To Breast Cancer

Study Links Certain Birth Control Pills To Breast Cancer

Newsy (Aug. 1, 2014) Previous studies have made the link between birth control and breast cancer, but the latest makes the link to high-estrogen oral contraceptives. Video provided by Newsy
Powered by NewsLook.com
Visitors Feel Part of the Pack at Wolf Preserve

Visitors Feel Part of the Pack at Wolf Preserve

AP (July 31, 2014) Seacrest Wolf Preserve on the northern Florida panhandle allows more than 10,000 visitors each year to get up close and personal with Arctic and British Columbian Wolves. (July 31) Video provided by AP
Powered by NewsLook.com
Florida Panther Rebound Upsets Ranchers

Florida Panther Rebound Upsets Ranchers

AP (July 31, 2014) With Florida's panther population rebounding, some ranchers complain the protected predators are once again killing their calves. (July 31) Video provided by AP
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