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Search tool for gene expression databases could uncover therapeutic targets, biological processes
Date:10/1/2013

ty worked with Bar-Joseph to develop ExpressionBlast and are co-authors of the journal report. Their intention was to develop a tool for gene expression queries that would be the equivalent of Blast, a two-decade-old tool for searching gene sequence databases that remains one of the most widely used tools in bioinformatics.

Genes encode the information necessary for life, while gene expression is the process by which that genetic information is transformed into proteins and by which genes are regulated. Understanding gene expression thus is critical for understanding biological and disease processes. This information is so important that, for the past decade or so, most leading journals have required researchers who publish papers on gene expression to submit their experimental data to public repositories such as GEO.

GEO alone holds data from more than 1 million microarrays. Each of these microarrays might contain up to 40,000 numerical values which indicate which genes are over- or underexpressed, and by how much. GEO and the European Bioinformatics Institute's ArrayExpress thus represent a treasure trove of potential discoveries. But existing searches are often dependent on keyword summaries submitted by each researcher, or require manual comparisons of microarrays.

ExpressionBlast uses novel, automated and scalable text analysis algorithms to transform the unstructured data in GEO so that it can be systematically searched. The researchers have thus far processed tens of thousands of expression series representing hundreds of thousands of individual arrays across several species. Once processed in this way, the data can be accessed easily via a graphical interface. This work was supported by a grant from the National Institutes of Health and a National Science Foundation Innovation Corps (I-Corps) award.


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Contact: Byron Spice
bspice@cs.cmu.edu
412-268-9068
Carnegie Mellon University
Source:Eurekalert

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