Navigation Links
Improved statistical tools reveal many linked loci

An innovative new statistical method, described in the open-access journal PLoS Biology, streamlines the computation required to identify all the potential locations in the genome that influence a particular physical trait, or phenotype. Thanks to the new method developed by John Storey, Joshua M. Akey, and Leonid Kruglyak, researchers have a more efficient genome-mining technique to help them identify all the genomic elements that produce specific traits.

In brewer's yeast alone, Storey and colleagues found that 37% of gene expression traits link to two loci, or positions in the genome.

"We were interested in being able to find combinations of genes that affect the phenotype," says Kruglyak. "It's generally thought that most traits of interest have a complex underlying genetic basis, but it's generally been pretty difficult to get at those." Typically, researchers might be able to find only one of the genetic factors, even though more than one genetic location contributes to the observed trait, such as blood pressure or cell growth.

The new statistical method bypasses the previously overwhelming computations needed to puzzle together the myriad elements that influence gene expression throughout an entire genome. And unlike earlier approaches to understanding how multiple loci interact, the new technique can distinguish between a group of genes with a linked subset and a group of genes with "joint linkage," where each gene site links to another.

"In some ways, it looks like you're complicating a problem because you're looking at thousands of genes instead of one trait," says Kruglyak. In reality, the method creates statistical conclusions that are more precise, he explains, because you're using so much data.

Storey et al. compared their method to another statistical method, called two-dimensional linkage analysis, which tests for linkage between all pairs of a large set of genomic marker sites. The authors found that two-dimens ional analysis is not only more computationally demanding than their new method, but also generates ambiguous results because it can be difficult to distinguish whether one or both of the loci being tested are responsible for altered expression levels. This problem grows exponentially with each added test site. This approach also failed to reveal that hierarchical relationships between two genomic locations control about one in seven yeast expression traits¡Xwhich Storey et al. discovered using their method.

Although the group studied yeast, their method can be applied to more complex organisms to search for even larger numbers of linked loci and to provide insights into the many interlocking pathways that make up the gene regulatory network.

Citation: Storey JD, Akey JM, Kruglyak L (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3(8): e267.


Source:PLoS Biology

Related biology news :

1. Improved Outcomes Releases GeneLinker(TM) Gold and Platinum Version 4.6
2. Improved predictions of warming-induced extinctions sought
3. Virginia Tech group adds tools to DNA-targeted anti-cancer drugs
4. New tools used to control foodborne hepatitis A outbreaks related to green onions
5. MWG Biotech expands siMAX?siRNA portfolio with new scales, lengths and design tools
6. Nanoparticles, nanoshells, nanotubes: How tiny specks may provide powerful tools against cancer
7. New RNAi tools enable systematic studies of gene function
8. Discovery of new molecular tools for biosynthesis could lead to advances in use of pectin
9. Recycled paper and compost could both be key tools to control plant disease
10. Nanotech tools yield DNA transcription breakthrough
11. Molecular tools make the cut
Post Your Comments:

(Date:4/14/2016)... 14, 2016 BioCatch ™, ... today announced the appointment of Eyal Goldwerger ... Goldwerger,s leadership appointment comes at a time ... the deployment of its platform at several of the ... which discerns unique cognitive and physiological factors, is a ...
(Date:3/31/2016)... March 31, 2016  Genomics firm Nabsys has completed ... Barrett Bready , M.D., who returned to the ... original technical leadership team, including Chief Technology Officer, ... Development, Steve Nurnberg and Vice President of Software and ... company. Dr. Bready served as CEO of ...
(Date:3/22/2016)... India , March 22, 2016 /PRNewswire/ ... market research report "Electronic Sensors Market for Consumer ... Proximity, & Others), Application (Communication & IT, ... Geography - Global Forecast to 2022", published ... industry is expected to reach USD 26.76 ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... DIEGO , June 27, 2016  Sequenom, Inc. ... committed to enabling healthier lives through the development of ... Court of the United States ... courts that the claims of Sequenom,s U.S. Patent No. ... patent eligibility criteria established by the Supreme Court,s Mayo ...
(Date:6/27/2016)... (PRWEB) , ... June 27, 2016 , ... Parallel ... clinical trials, announced today the Clinical Reach Virtual Patient Encounter CONSULT module ... circle with the physician and clinical trial team. , Using the CONSULT module, patients ...
(Date:6/27/2016)... (PRWEB) , ... June 27, 2016 , ... ... operations for Amgen, will join the faculty of the University of North ... adjunct professor of strategy and entrepreneurship at UNC Kenan-Flagler, with a focus on ...
(Date:6/27/2016)... June 27, 2016   Ginkgo Bioworks , a ... engineering, was today awarded as one of the ... the world,s most innovative companies. Ginkgo Bioworks is ... the real world in the nutrition, health and ... directly with customers including Fortune 500 companies to ...
Breaking Biology Technology: