Featured Research

from universities, journals, and other organizations

Bioinformatics: We can learn a lot from other species

Date:
May 17, 2012
Source:
Swiss Institute of Bioinformatics
Summary:
Researchers have confirmed the long-held belief that studying the genes we share with other animals is useful. The study shows how bioinformatics makes it possible to test the fundamental principles on which life science is built.

Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held belief that studying the genes we share with other animals is useful. The study, published May 17 in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the fundamental principles on which life science is built.

Studying genes helps life science researchers understand how our bodies work and how diseases progress. Scientists have long looked to model species -- mice, for example -- to understand human biology. This is at the root of what is called the 'ortholog conjecture': the idea that we can take what we learn from a few species and apply it to many.

The ortholog conjecture

To get an idea of what orthologs are about, consider wolf teeth. If we want to know more about our canine teeth, would we learn more by looking at the canines of wolves? Or would it be better to look at our molars? The answer might not be straightforward. In genetics, scientists address a similar question: Is it better to compare genes in mice and humans that directly descend from a common ancestor (these are called 'orthologs') -- or to compare imperfect copies of genes within a human being (the 'paralogs')?

Assume nothing

For the past 40 years, scientists have gone with Plan A: the orthologs, and this has worked quite well. Studying genes in model species has provided invaluable insights in all areas of biology. But until now, there hasn't been enough data to answer this question with authority. With advances in biotechnology producing vast quantities of data every day, there is finally enough to settle the debate.

Using advanced computational techniques on data derived from tens of thousands of scientific articles, the researchers analysed 400 000 pairs of genes (orthologs and paralogs) from 13 different species. The team compared the two approaches and picked a winner.

"We have the data to prove that the study of orthologs is indeed useful, but we are only at the beginning," says Prof. Marc Robinson-Rechavi of SIB and the University of Lausanne. "This is at the heart of all of comparative genomics, in which we try to extrapolate knowledge from a handful of organisms and apply it to all of life."

"We found that current experimental annotations do support the standard model," explains Christophe Dessimoz of EMBL-EBI. "Our work corroborates the assumption that studying the genes of other species -- whether mice, yeast, or even bacteria -- can elucidate aspects of human biology."

The same question has recently been addressed by Matthew Hahn and colleagues (University of Indiana, USA), whose different conclusion sparked some debate. The new research demonstrates that these controversial results were due to overlooked biases in the collective knowledge of gene function. Controlling for these, the new study unequivocally supports the ortholog conjecture and the fact that studying species we are only distantly related to -- even worms, flies, yeasts or bacteria -- is relevant and useful.

This study was made possible by the tradition of open science in bioinformatics, which is strongly supported by SIB, EMBL-EBI and ELIXIR, the incipient infrastructure for life science data in Europe. All of the data used in the study was freely available, including the genome sequences and experimental knowledge described in thousands of publications. ELIXIR will build on this tradition and provide the next generation of infrastructure for biological information in Europe and worldwide.


Story Source:

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


Journal Reference:

  1. Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz. Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs. PLoS Computational Biology, 2012; 8 (5): e1002514 DOI: 10.1371/journal.pcbi.1002514

Cite This Page:

Swiss Institute of Bioinformatics. "Bioinformatics: We can learn a lot from other species." ScienceDaily. ScienceDaily, 17 May 2012. <www.sciencedaily.com/releases/2012/05/120517192929.htm>.
Swiss Institute of Bioinformatics. (2012, May 17). Bioinformatics: We can learn a lot from other species. ScienceDaily. Retrieved October 22, 2014 from www.sciencedaily.com/releases/2012/05/120517192929.htm
Swiss Institute of Bioinformatics. "Bioinformatics: We can learn a lot from other species." ScienceDaily. www.sciencedaily.com/releases/2012/05/120517192929.htm (accessed October 22, 2014).

Share This



More Plants & Animals News

Wednesday, October 22, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Working Mother DIY: Pumpkin Pom-Pom

Working Mother DIY: Pumpkin Pom-Pom

Working Mother (Oct. 22, 2014) How to make a pumpkin pom-pom. Video provided by Working Mother
Powered by NewsLook.com
San Diego Zoo's White Rhinos Provide Hope for the Critically Endangered Species

San Diego Zoo's White Rhinos Provide Hope for the Critically Endangered Species

Reuters - Light News Video Online (Oct. 22, 2014) The pair of rare white northern rhinos bring hope for their species as only six remain in the world. Elly Park reports. Video provided by Reuters
Powered by NewsLook.com
Raw: Bear Cub Strolls Through Oregon Drug Store

Raw: Bear Cub Strolls Through Oregon Drug Store

AP (Oct. 22, 2014) Shoppers at an Oregon drug store were surprised by a bear cub scurrying down the aisles this past weekend. (Oct. 22) Video provided by AP
Powered by NewsLook.com
Family Pleads for Pet Pig to Stay at Home

Family Pleads for Pet Pig to Stay at Home

AP (Oct. 22, 2014) The Johnson family lost their battle with the Chesterfield County, Virginia Planning Commission to allow Tucker, their pet pig, to stay in their home, but refuse to let the board keep Tucker away. (Oct. 22) 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:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

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