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Beyond Bioinformatics |
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Title |
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Under-representation of PolyA/PolyT tailed ESTs in Human ESTdb: an obstacle to alternative polyadenylation inference
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Authors |
Roi Gilat, Sergey Goncharov, Nir Esterman and Dorit Shweiki*
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Affiliation |
Bioinformatics Program, School of Computer Science, The Academic College of Tel Aviv-Yaffo, Tel Aviv, Israel
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dorits@mta.ac.il; * Corresponding author
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Phone |
+972-3-5211853
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Fax |
+972-3-5211871
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Article Type |
Hypothesis
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Date |
received September 05, 2006; revised October 02,2006; accepted October 02, 2006; published online October 07, 2006
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Abstract |
Alternative polyadenylation is a key regulatory process which affects the 3' end formation of variants of the same transcription unit, thus altering gene expression pattern, and transcripts' cellular behaviour and characteristics. The common methodology for computational analysis of alternative polyadenylation signal utilization is based on EST data, specifically on PolyA/PolyT tailed ESTs. Studying the human ESTs dataset we detected a significant under-representation of PolyA/PolyT tailed ESTs, constituting only 10% of most libraries. Consequently, more than 50% of false-negative events are revealed in the analysis of alternatively polyadenylated variants' expression. We therefore argue that the ratios of PolyA/PolyT tailed ESTs, as represented in the human EST database, do not reflect the true-picture of 3' end variants formation of a given physiological situation. Thus the EST database should not be considered a reliable source for alternative polyadenylation signal usage inference.
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Keywords
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polyadenylation; human EST; PolyA/PolyT; alternative polyadenylation inference |
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Citation |
Gilat et al., Bioinformation 1(6): 220-224 (2006)
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics Publishing Group
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Copyright |
Publisher
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Copyright Transfer Statement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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