Open Access Highly Accessed Methodology article

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

Amandine Bemmo13, David Benovoy23, Tony Kwan23, Daniel J Gaffney23, Roderick V Jensen4 and Jacek Majewski23*

Author Affiliations

1 Universite de Montreal, Montreal, QC, Canada

2 Department of Human Genetics, McGill University, Montreal, QC, Canada

3 McGill University and Genome Quebec Innovation Center, Montreal, QC, Canada

4 Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA

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BMC Genomics 2008, 9:529  doi:10.1186/1471-2164-9-529

Published: 7 November 2008

Additional files

Additional file 1:

Examples of discordance between platforms. The data is visualized using custom tracks within the UCSC genome browser. We also show the location of U133 and Illumina probes for each gene. The table gives the fold change and significance levels for each platform. A. KISS1R, probable polyadenylation difference. WT profiling indicates that the expression change of the coding sequence of the gene is actually in the opposite direction to the change detected by 3' profiling. B. CRTAC1. A whole transcript change which is only detected by the Exon Array, most likely because the 3' methods target a non-variable UTR region. C. PSD3. Expression change detected by all three platforms, but the Exon Array identifies the nature of the isoform change – annotated alternative promoter usage. D. BCAS1. A putative alternative promoter (not annotated) indicated by the Exon Array.

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Additional file 2:

UCSC browser links illustrating probeset level expression differences (fold-change and p-values) for the top 100 isoforms differentially expressed between the brain and reference samples, obtained from the probeset level analysis.

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Additional file 3:

UCSC browser links illustrating the probeset level expression differences (fold-change and p-values) as well as the normalized (SI) differences for the top 100 isoforms differentially expressed between the brain and reference samples, obtained from the Splicing Index analysis.

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Open Data