Title

Under-representation of PolyA/PolyT tailed ESTs in Human ESTdb: an obstacle to alternative polyadenylation inference

Authors

Roi Gilat, Sergey Goncharov, Nir Esterman and Dorit Shweiki*

Affiliation

Bioinformatics Program, School of Computer Science, The Academic College of Tel Aviv-Yaffo, Tel Aviv, Israel

Email

dorits@mta.ac.il; * Corresponding author

Phone

+972-3-5211853

Fax

+972-3-5211871

Article Type

Hypothesis

Date

received September 05, 2006; revised October 02,2006; accepted October 02, 2006; published online October 07, 2006

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.

Keywords

polyadenylation; human EST; PolyA/PolyT; alternative polyadenylation inference

Citation

Gilat et al., Bioinformation 1(6): 220-224 (2006)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.