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New Stanford tool enables wider analyses of genome 'deep sequencing'
Date:5/2/2010

nter a list of all the binding sites they've found throughout the genome for their transcription factor of interest. No prescreening is necessary, and the list can be hundreds or thousands of items long. Some will be biologically meaningful, and some will be experimental flukes. The software program will then provide an analysis revealing not only which genes that transcription factor is likely to moderate, both near and far, but also in which developmental or molecular pathways it is likely to function.

"The analysis gets pushed back into the hands of the person who did the experiment," said Bejerano. "Now you will start to see the kinds of results that we had expected with this much data." He and his collaborators found that test runs with well-known transcription factors verified the factors' association with the expression of particular genes, but also identified new, previously unsuspected alliances between binding sites and genes separated on the DNA by up to 1 million nucleotides.

"We've been asking the right questions, but using the wrong interpretation tools to answer them," said Bejerano. "We don't expect that this tool will help three labs. We expect that it will help 3,000 labs. GREAT can look at thousands of binding sites and tell you things that your transcription factor is doing that have never been reported before."


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Contact: Krista Conger
kristac@stanford.edu
650-725-5371
Stanford University Medical Center
Source:Eurekalert

Page: 1 2 3

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