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Getting More From Whole-Transcript Microarrays
Date:5/22/2009

MELBOURNE, Australia , May 22 /PRNewswire/ -- The widely-used Affymetrix Whole-Transcript Gene 1.0 ST (sense target) microarray platform, normally used to assay gene expression, can also be utilized to interrogate exon-specific splicing. Research published today in the open access journal BMC Bioinformatics shows scientists how to monitor alternative splicing activity on a genome-wide scale, without investing in new exon microarray technologies.

Alternative splicing produces a variety of mRNA transcripts from a single gene by splicing together different combinations of exons, which can give rise to alternative protein forms that are functionally distinct. Almost 90% of human genes are now considered to exhibit alternative splicing and to meet the demand to analyse this on a genome-wide scale, Affymetrix have developed their Exon 1.0 ST platform. However, the study by Mark Robinson and Terence Speed from the University of Melbourne and the Walter and Eliza Hall Institute of Medical Research in Australia suggests that the gene platform can also do the job.

The scientists explored a publicly available dataset of 11 human tissues that were analyzed on both the Affymetrix Gene 1.0 ST and the Affymetrix Exon 1.0 ST chips. Robinson said, "Our intention was not to provide a detailed comparison between those platforms and to suggest that the Gene array should be used as a replacement for the Exon arrays. We simply wanted to demonstrate that researchers could get information about differential splicing from the Gene platform in certain circumstances at no additional experimental cost. We, therefore, provide added value to their collected data."

The authors acknowledge that the ability to detect differential splicing depends on various factors, including the number of probes covering the gene and the nature of the splicing event. They constructed a new statistical method, called FIRMAGene, that uses informati
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SOURCE Walter and Eliza Hall Institute of Medical Research
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