FIRMA: a Method for Detection of Alternative Splicing from Exon Array Data

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2008 Jun 25

PMID 18573797

Citations 79

Authors

E Purdom

K M Simpson

M D Robinson

J G Conboy

A V Lapuk

T P Speed

Affiliations

Soon will be listed here.

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.

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