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.
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.
Authors: Gene W Yeo; Eric Van Nostrand; Dirk Holste; Tomaso Poggio; Christopher B Burge Journal: Proc Natl Acad Sci U S A Date: 2005-02-11 Impact factor: 11.205
Authors: Keith Le; Katherine Mitsouras; Meenakshi Roy; Qi Wang; Qiang Xu; Stanley F Nelson; Christopher Lee Journal: Nucleic Acids Res Date: 2004-12-14 Impact factor: 16.971
Authors: Melissa S Cline; John Blume; Simon Cawley; Tyson A Clark; Jing-Shan Hu; Gang Lu; Nathan Salomonis; Hui Wang; Alan Williams Journal: Bioinformatics Date: 2005-06 Impact factor: 6.937
Authors: Dorothea Emig; Nathan Salomonis; Jan Baumbach; Thomas Lengauer; Bruce R Conklin; Mario Albrecht Journal: Nucleic Acids Res Date: 2010-05-31 Impact factor: 16.971
Authors: Nathan Salomonis; Brandon Nelson; Karen Vranizan; Alexander R Pico; Kristina Hanspers; Allan Kuchinsky; Linda Ta; Mark Mercola; Bruce R Conklin Journal: PLoS Comput Biol Date: 2009-11-06 Impact factor: 4.475
Authors: Carla S Moller-Levet; Guy N J Betts; Adrian L Harris; Jarrod J Homer; Catharine M L West; Crispin J Miller Journal: PLoS Comput Biol Date: 2009-11-20 Impact factor: 4.475