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

FIRMA: a method for detection of alternative splicing from exon array data. Research Abstract Details 

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

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.

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

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Bioinformatics (Oxford, England)

VOLUME: 24

Page Numbers: 1707-14

Journal Abbreviation: Bioinformatics

ISSN: 1460-2059

DAY: 23

MONTH: 06

YEAR: 2008

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

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LANGUAGE: eng

NlmUniqueID: 9808944

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Grant and Affiliation Information for FIRMA: a method for detection of alternative splicing from exon array data.

AFFILIATION: Department of Statistics, University of California at Berkeley, 367 Evans Hall #3860, Berkeley, CA 94720-3860, USA. epurdom@stat.berkeley.edu

Country: England

AGENCY: United States NCI

GRANT: U24 CA126551-01

ACRONYM: CA

MEDLINETA: Bioinformatics

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