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

Purdom, E.; Simpson, K. M.; Robinson, M. D.; Conboy, J. G.; Lapuk, A. V.; Speed, T. P.

doi:10.1093/bioinformatics/btn284

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

Journal Article · Mon Jun 23 00:00:00 EDT 2008 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btn284· OSTI ID:1625258

Purdom, E. ^[1]; Simpson, K. M. ^[2]; Robinson, M. D. ^[3]; Conboy, J. G. ^[4]; Lapuk, A. V. ^[4]; Speed, T. P. ^[5]

Univ. of California, Berkeley, CA (United States). Dept. of Statistics; DOE/OSTI
The Walter and Eliza Hall Inst., Parkville, VIC (Australia)
The Walter and Eliza Hall Inst., Parkville, VIC (Australia); Univ. of Melbourne (Australia). Dept. of Medical Biology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division
Univ. of California, Berkeley, CA (United States). Dept. of Statistics; The Walter and Eliza Hall Inst., Parkville, VIC (Australia)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of California, Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625258

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 15 Vol. 24; ISSN 1367-4803

Publisher:: International Society for Computational Biology - Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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