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Bioinformatics Advance Access published online on August 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl429
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received April 11, 2006
Revised July 5, 2006
Accepted August 1, 2006

Article

A large quantity of novel human antisense transcripts detected by LongSAGE

Xijin Ge 1, Qingfa Wu 1, Yong-Chul Jung 1, Jun Chen 1, and San Ming Wang 2 *

1 Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, 1001 University Place, Evanston, IL 60201 USA
2 Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, 1001 University Place, Evanston, IL 60201 USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 1001 University Place, Evanston, IL 60201 USA

* To whom correspondence should be addressed.
San Ming Wang, E-mail: swang1{at}northwestern.edu


  Abstract

Motivation: Taking advantage of the high sensitivity and specificity of LongSAGE tag for transcript detection and genome mapping, we analyzed the 632,813 unique human LongSAGE tags deposited in public databases to identify novel human antisense transcripts.

Results: Our study identified 45,321 tags that match the antisense strand of 9,804 known mRNA sequences, 6,606 of which contain antisense ESTs and 3,198 are mapped only by SAGE tags. Quantitative analysis showed that the detected antisense transcripts are present at levels lower than their counterpart sense transcripts. Experimental results confirmed the presence of antisense transcripts detected by the antisense tags. We also constructed an antisense tag database that can be used to identify the antisense SAGE tags originated from the antisense strand of known mRNA sequences included in the RefSeq database.

Conclusions: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts, and demonstrates the prevalence of antisense transcripts in the human genome.

Associate Editor: Nikolaus Rajewsky
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