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Bioinformatics Advance Access published online on December 7, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti205
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 4, 2004
Revised November 23, 2004
Accepted December 2, 2004

Article

LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome

Matthias B. Wahl 1, Ulrich Heinzmann 2, and Kenji Imai 1*

1 Institute of Developmental Genetics, GSF-National Research Center for Environment and Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
2 Institute of Pathology, GSF-National Research Center for Environment and Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany

* To whom correspondence should be addressed.
Kenji Imai, E-mail: imai{at}gsf.de


  Abstract

Motivation: Despite the increasing notions to the functional importance of antisense transcripts in gene regulation, the genome-wide overview on the ontology of antisense genes has not been obtained. Therefore, we tried to find novel antisense genes genome-wide by using our LongSAGE dataset of 202,015 tags (consisting of 41,718 unique tags), experimentally generated from mouse embryonic tail libraries.

Results: We identified 1,260 potential antisense genes, of which 1001 are not annotated in EnsEMBL, thereby being regarded as novel. Interestingly their sense counterparts were co-expressed in the majority of the cases.

Conclusions: The use of LongSAGE transcriptome data is extremely powerful in the identification of thus-far unknown antisense transcripts, even in the case of well-characterized organisms like the mouse.


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