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Bioinformatics Advance Access originally published online on December 7, 2004
Bioinformatics 2005 21(8):1389-1392; doi:10.1093/bioinformatics/bti205
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

Motivation: Despite the increasing notions of 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 1260 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.

Contact: imai{at}gsf.de


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