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Gene function discovery: Guilt by association
Date:1/31/2010

Palo Alto, CAScientists have created a new computational model that can be used to predict gene function of uncharacterized plant genes with unprecedented speed and accuracy. The network, dubbed AraNet, has over 19,600 genes associated to each other by over 1 million links and can increase the discovery rate of new genes affiliated with a given trait tenfold. It is a huge boost to fundamental plant biology and agricultural research.

Despite immense progress in functional characterization of plant genomes, over 30% of the 30,000 Arabidopsis genes have not been functionally characterized yet. Another third has little evidence regarding their role in the plant.

"In essence, AraNet is based on the simple idea that genes that physically reside in the same neighborhood, or turn on in concert with one another are probably associated with similar traits," explained corresponding author Sue Rhee at the Carnegie Institution's Department of Plant Biology. "We call it guilt by association. Based on over 50 million scientific observations, AraNet contains over 1 million linkages of the 19,600 genes in the tiny, experimental mustard plant Arabidopsis thaliana. We made a map of the associations and demonstrated that we can use the network to propose that uncharacterized genes are linked to specific traits based on the strength of their associations with genes already known to be linked to those characteristics."

The network allows for two main types of testable hypotheses. The first uses a set of genes known to be involved in a biological process such as stress responses, as a "bait" to find new genes ("prey") involved in stress responses. The bait genes are linked to each other based on over 24 different types of experiments or computations. If they are linked to each other much more frequently or strongly than by chance, one can hypothesize that other genes that are as well linked to the bait genes have a high probability of bein
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Contact: Sue Rhee
rhee@acoma.stanford.edu
650-325-1521
Carnegie Institution
Source:Eurekalert  

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