Applied Bioinformatics

, Volume 5, Issue 4, pp 249–253 | Cite as

Alternative mRNA Polyadenylation Can Potentially Affect Detection of Gene Expression by Affymetrix GeneChip® Arrays

  • Veera D’mello
  • Ju Youn Lee
  • Clinton C. MacDonald
  • Bin Tian
Biomedical Genomics and Proteomics


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.


Affymetrix GeneChip Exon Array Alternative Polyadenylation Terminal Exon Affymetrix Microarray Suite 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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.


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Copyright information

© Adis Data Information BV 2006

Authors and Affiliations

  • Veera D’mello
    • 1
  • Ju Youn Lee
    • 1
  • Clinton C. MacDonald
    • 2
  • Bin Tian
    • 1
  1. 1.Department of Biochemistry and Molecular Biology, New Jersey Medical SchoolUniversity of Medicine and Dentistry of New JerseyNewarkUSA
  2. 2.Department of Cell Biology and BiochemistryTexas Tech University Health Sciences CenterLubbockUSA

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