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:12/8/2016)... , Dec. 8, 2016  Valeant Pharmaceuticals ... TSX: VRX) ("Valeant") today announced positive results from ... study to assess the safety and efficacy of ... treatment of plaque psoriasis. Within ... with moderate to severe psoriasis, IDP-118 showed statistical ...
(Date:12/8/2016)... FRISCO, Texas , Dec. 8, 2016 /PRNewswire/ ... new program that brings leading-edge laboratory services and ... the United States , allowing more doctors ... and health care management solutions. Logo ... Hospital systems, under pressure to ...
(Date:12/8/2016)... , December 8, 2016 Information products ... metrics in Scopus , the world,s largest abstract ... access to comprehensive metrics for journals from over 5,000 publishers. The ... which journals to subscribe to and when to adjust a journal,s ... , , ...
Breaking Medicine Technology:
(Date:12/9/2016)... ... 09, 2016 , ... An inventor from Cana, Va., wanted to fulfill the ... amusement park rides. , The patent-pending SAFETY STRAP FOR AMPUTEES improves accessibility. It eliminates ... be set up in a matter of minutes, or even seconds. The SAFETY STRAP ...
(Date:12/9/2016)... PA (PRWEB) , ... December 09, 2016 , ... "I ... said an inventor from Winchester, Va. "I thought that if the nebulizer had a ... treatments rather than fearing them." , He developed the patent-pending NEBY to avoid the ...
(Date:12/8/2016)... ... December 08, 2016 , ... After enjoying record-breaking ... registration today for its 33rd Annual Issues & Research Conference, March 2-3, ... theme of the conference is “Persistent Challenges and New Opportunities: Using Research to ...
(Date:12/8/2016)... ... December 08, 2016 , ... Mirixa Corporation ... adherence, and other pharmacist-delivered patient care services, has announced the promotions of Karen ... to vice president of sales. , Litsinger joined Mirixa in 2008 after ...
(Date:12/8/2016)... ... December 08, 2016 , ... Premier Fitness Camp (PFC) ... , the ultimate weight loss and wellness program, at their world headquarters of Omni ... provide immediate and long-term results to anyone seeking weight loss, personal development, a healthy ...
Breaking Medicine News(10 mins):