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:2/4/2016)... Calif. , Feb. 4, 2016  Edwards Lifesciences ... patient-focused innovations for structural heart disease and critical care ... accelerated share repurchase (ASR) agreement with Morgan Stanley & ... stock.  This repurchase is part of the Company,s previously ... the Company,s common stock.  --> ...
(Date:2/4/2016)... Feb. 4, 2016 Worldwide Radiology Oncology ... growth as next generation systems provide a way ... for cancer surgery. New systems pinpoint the delivery ... has been such a problem previously, limiting the ... robots take cancer surgery far beyond what has ...
(Date:2/4/2016)... Calif. , Feb. 4, 2016  SciClone ... today announced it has entered into a settlement ... Commission (SEC) fully resolving the SEC,s investigation into ... (FCPA).  Under the terms of the settlement agreement, ... $12.8 million, including disgorgement, pre-judgment interest and a ...
Breaking Medicine Technology:
(Date:2/5/2016)... ... February 05, 2016 , ... Freed-Hardeman University President Joe ... signed a joint enrollment and degree completion agreement. The agreement, which begins ... degrees at FHU|Dickson. , The agreement allows students to be jointly admitted ...
(Date:2/5/2016)... ... February 05, 2016 , ... In the fourth ... country gathered at the La Valencia Hotel in San Diego, California to discuss ... named the year’s most outstanding franchise, walking away with the coveted David Wright ...
(Date:2/5/2016)... SARASOTA, Fla., (PRWEB) , ... February 05, 2016 , ... ... appetizing recipes just in time for this weekend’s Big Game. Take the stress out ... ingredients that will keep your guests happy at every stage of the game. , ...
(Date:2/5/2016)... ... February 05, 2016 , ... Stuart Bentkover, MD, FACS is ... to provide the most effective tattoo removal today, Dr. Bentkover is the only doctor ... by Cynosure, the PicoSure has been approved by the Food and Drug Administration (FDA) ...
(Date:2/5/2016)... ... February 05, 2016 , ... Health and wellness is a topic that should ... event they are experiencing an illness. Migraines are a severe form of a headache ... migraines would not wish the pain on their worst enemy, the feeling can last ...
Breaking Medicine News(10 mins):