Journal
BIOINFORMATICS
Volume 24, Issue 15, Pages 1707-1714Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btn284
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Funding
- NCI NIH HHS [U24 CA126551-01] Funding Source: Medline
- NHLBI NIH HHS [R01 HL045182] Funding Source: Medline
- NIDDK NIH HHS [R21 DK075021] Funding Source: Medline
- NIGMS NIH HHS [R01 GM083084, 5R01GM083084, R01 GM083084-01] Funding Source: Medline
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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.
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