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SAGE Genie Manages Gene Expression Data

31 July 2002. Over the past decade, new technologies have led to an explosion in the generation of biological data, leaving scientists wishing for a simple way to assimilate and then present the new information in an easily understandable format. As reported in the July 15 PNAS early edition, at least some of those wishes may be granted by the SAGE Genie.

The SAGE Genie is a new set of tools for managing data generated by Serial Analysis of Gene Expression (SAGE)-a technique used to measure levels of large numbers of RNA transcripts (see Velculescu, et al.). The tools, managed by the Cancer Genome Anatomy Project, are freely available online, and as demonstrated by Gregory Riggins, Duke University Medical Center, and colleagues, allow the user to readily identify differences between genes expressed in diseased and normal human tissues.

At the heart of the Genie is the SAGE Anatomic Viewer which links data from over five million independently identified transcripts with over 100 tissue types. The expression of a given transcript can then be matched with tissues or organs and displayed using an extremely intuitive graphic interface. The investigators sifted through the SAGE data to find those transcripts that are definitively expressed in human tissue and extended the SAGE analysis to malignant cells. The Anatomic Viewer presents color-coded expression levels for each transcript for a multitude of tissues, including brain, pancreas, breast, etc., and allows malignancy and expression to be matched at a glance.

Users can test drive the Genie at http://cgap.nci.nih.gov/SAGE.—Tom Fagan.

Reference:
Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, de Souza SJ, Riggins GJ. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002 Aug 20 ; 99(17):11287-92. Abstract

Reference:Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, de Souza SJ, Riggins GJ. An anatomy of normal and malignant gene expression. Proc Natl Acad Sci U S A. 2002 Aug 20 ; 99(17):11287-92. Abstract

 
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