Skip Navigation


Bioinformatics Advance Access originally published online on June 23, 2008
Bioinformatics 2008 24(15):1707-1714; doi:10.1093/bioinformatics/btn284
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
24/15/1707    most recent
btn284v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Purdom, E.
Right arrow Articles by Speed, T.P.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Purdom, E.
Right arrow Articles by Speed, T.P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FIRMA: a method for detection of alternative splicing from exon array data

E. Purdom 1,*, K. M. Simpson 2, M. D. Robinson 2,3, J. G. Conboy 4, A. V. Lapuk 4 and T.P. Speed 1,2

1Department of Statistics, University of California at Berkeley, 367 Evans Hall #3860, Berkeley, CA 94720–3860, USA, 2The Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Victoria, 3050, 3Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia and 4Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: Analyses of EST data show that alternative splicing is much more widespread than once thought. The advent of exon and tiling microarrays means that researchers now have the capacity to experimentally measure alternative splicing on a genome wide level. New methods are needed to analyze the data from these arrays.

Results: We present a method, finding isoforms using robust multichip analysis (FIRMA), for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle be extended to other exon arrays, tiling arrays or splice junction arrays. We have evaluated the method using simulated data, and have also applied it to two datasets: a panel of 11 human tissues and a set of 10 pairs of matched normal and tumor colon tissue. FIRMA is able to detect exons in several genes confirmed by reverse transcriptase PCR.

Availability: R code implementing our methods is contributed to the package aroma.affymetrix.

Contact: epurdom{at}stat.berkeley.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: David Rocke

Received on February 25, 2008; revised on May 18, 2008; accepted on June 6, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.