Getting More from Whole-Transcript Microarrays
MELBOURNE, May 22 /Medianet International-AsiaNet/ --
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 information about
adjacent poorly fitting probes to calculate differential expression in the Gene arrays and showed
that it provides comparable results to the Exon array analysis. The approach can only be used in
well-annotated genes and can detect differential splicing involving multiple exons. However, they
suggested that it should work particularly well for genes containing few exons, since for these
genes the coverage of probes in the Gene platform can be greater than the Exon platform.
Dr Robinson added that, “To the best of our knowledge, this is the first statistical method that
interrogates differential splicing using the Gene 1.0 ST platform. We have used this method for
uncovering differential splicing in human tissues, where typically a small number of tissues exhibit a
distinct pattern. However, we believe it could be useful in a variety of experimental settings.”
FIRMAGene can be applied to human, mouse and rat samples, for which the latest Affymetrix Gene
1.0 ST platforms are available, or any other whole-transcript microarray design.
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The Walter and Eliza Hall Institute is one of the world’s leading biomedical research centres.
Established in 1915 and affiliated with The University of Melbourne and The Royal Melbourne
Hospital, the Institute's mission is ‘Mastery of Disease through Discovery’. Its world-renowned
research teams have been responsible for breakthrough science and pioneering therapies that have
changed the face of disease and human health worldwide. Today they are focused on four big
global medical challenges: cancer, immunity, autoimmunity and infectious diseases. The Walter and
Eliza Hall Institute is located at Parkville, Victoria where it will soon be housed in a state-of-the-art
new building.
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SOURCE: Walter and Eliza Hall Institute of Medical Research
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