Navigation Links
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 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.

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.

       CONTACT: Michelle Trevorrow
                Head, Fundraising, Communications and External Relations
                Ph: +61 3 9345 2639
                Mob: +61 400 603 150
                email: trevorrow@wehi.edu.au


'/>"/>
SOURCE Walter and Eliza Hall Institute of Medical Research
Copyright©2009 PR Newswire.
All rights reserved

Related medicine technology :

1. New UNAIDS Report Offers Encouraging News, But Most HIV-Positive Mothers Still Not Getting the Care & Treatment They Need
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:4/27/2016)... April 27, 2016 Tie-up with ... initiative to save newborns   Fortis ... & newborns in collaboration with Breast Milk Foundation (BMF), a ... Pasteurized Human Milk Bank, ,Amaara, in Delhi-NCR today. This non-profit ... source for infants and should be available to babies deprived ...
(Date:4/27/2016)... YORK , April 27, 2016 ... OASM ), a developer of a new generation ... announced positive overall survival results for Paclical/Apealea in ... of 789 patients with epithelial ovarian cancer. These ... groups: Paclical/Apealea in combination with carboplatin versus Taxol ...
(Date:4/26/2016)... Diplomat Pharmacy, Inc. (NYSE: DPLO) is pleased ... Pharm D., to Vice President of Education and Quality. ... will continue to lead and oversee Diplomat University, an ... and training to Diplomat employees and external professionals on ... also houses the quality assurance department, which focuses on ...
Breaking Medicine Technology:
(Date:4/29/2016)... ... April 29, 2016 , ... In an article ... shares her enthusiasm for Botox and lip injections, which she underwent in order to ... Coachella Valley Music and Arts Festival. The article explains that Ms. Mirmelli’s situation is ...
(Date:4/29/2016)... ... , ... Our bodies are bombarded daily by environmental and lifestyle factors that ... is to adopt a more healthful diet, but too many people think that food ... Nutritionist and the creator of the Newport Beach Cleanse and 14-Day Eating Plan, disagrees ...
(Date:4/29/2016)... ... April 29, 2016 , ... The White House announced ... loans, more information about their loan terms and accounts, and more protections for ... including federal and private loans, has reached $1.3 trillion, with 43 million Americans ...
(Date:4/29/2016)... ... ... Spine Team Texas, a comprehensive spine physician group specializing in the treatment ... been invited to be a featured speaker at the Texas Society of the American ... 2016. , Dr. R. Scott McPherson, a physical medicine and rehabilitation specialist, will ...
(Date:4/29/2016)... , ... April 29, 2016 , ... ... Canadian Celiac Association (CCA), is pleased to announce the launch of the ... nutritional articles, recipes, and more. The purpose of the GFCP Scoop ...
Breaking Medicine News(10 mins):