Alternative mRNA Polyadenylation Can Potentially Affect Detection of Gene Expression by Affymetrix GeneChip® Arrays
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DNA microarrays have been widely used to examine gene expression. The Affymetrix GeneChip® is one of the most commonly used platforms, employing DNA probes of 25 nucleotides designed to hybridise to different regions of target mRNA. The targeted region is often biased toward the 3′ end of mRNA, which can lead to biases in detection. A large number of mammalian genes can undergo alternative polyadenylation under different cellular conditions. Multiple polyadenylation sites can lead to variable transcripts with different hybridisation properties. Here, we surveyed probes on human, mouse and rat GeneChip® arrays and found that the detection of a significant proportion of mRNAs can potentially be affected by alternative polyadenylation. This could lead to inaccurate interpretation of GeneChip® data when the changes of expression values actually result from alternative use of polyadenylation sites.
KeywordsAffymetrix GeneChip Exon Array Alternative Polyadenylation Terminal Exon Affymetrix Microarray Suite
We thank Yixin Wang from Veridex, and Haibo Zhang and Jianghui Liu at the University of Medicine and Dentistry of New Jersey (UMDNJ) for helpful discussions. Bin Tian was supported by the Foundation of UMDNJ. Clinton C MacDonald was supported by Grants R01 HD37109-04 and K02 HD047387-02 from the National Institutes of Health.
The authors have no conflicts of interest that are directly relevant to the content of this article.
- 5.Affymetrix Microarray Suite User’s Guide [online]. Available from URL: http://www.affymetrix.com/support/technical/manuals.affx [Accessed 2006 Sep 21]
- 7.Wang H, Hubbell E, Hu JS, et al. Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics 2003; 19Suppl. 1: 1315–22Google Scholar