Research article

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences

Joseph C Lee¹ , David Stiles¹ , Jun Lu¹ and Margaret C Cam^1,2

¹Genomics Core Laboratory, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA

²Office of the Director, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA

author email corresponding author email

BMC Genomics 2007, 8:284doi:10.1186/1471-2164-8-284

Published:	20 August 2007

Abstract

Background

Microarrays are a popular tool used in experiments to measure gene expression levels. Improving the reproducibility of microarray results produced by different chips from various manufacturers is important to create comparable and combinable experimental results. Alternative splicing has been cited as a possible cause of differences in expression measurements across platforms, though no study to this point has been conducted to show its influence in cross-platform differences.

Results

Using probe sequence data, a new microarray probe/transcript annotation was created based on the AceView Aug05 release that allowed for the categorization of genes based on their expression measurements' susceptibility to alternative splicing differences across microarray platforms. Examining gene expression data from multiple platforms in light of the new categorization, genes unsusceptible to alternative splicing differences showed higher signal agreement than those genes most susceptible to alternative splicing differences. The analysis gave rise to a different probe-level visualization method that can highlight probe differences according to transcript specificity.

Conclusion

The results highlight the need for detailed probe annotation at the transcriptome level. The presence of alternative splicing within a given sample can affect gene expression measurements and is a contributing factor to overall technical differences across platforms.