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Nucleic Acids Research 2005 33(3):e26; doi:10.1093/nar/gni025
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Published online 16 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Reproducibility, bioinformatic analysis and power of the SAGE method to evaluate changes in transcriptome

S. Dinel, C. Bolduc, P. Belleau, A. Boivin, M. Yoshioka, E. Calvo, B. Piedboeuf, E. E. Snyder1, F. Labrie and J. St-Amand*

Oncology and Molecular Endocrinology Research Center, Laval University Medical Center, Department of Anatomy and Physiology, Université Laval Québec, Canada 1 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0477, USA

*To whom correspondence should be addressed at Functional Genomics Laboratory, Oncology and Molecular Endocrinology Research Center, Laval University Hospital Center (CHUL) 2705, boulevard Laurier, Québec, Canada G1V 4G2. Tel: +1 418 654 2296; Fax: +1 418 654 2761; Email: Jonny.St-Amand{at}crchul.ulaval.ca

Received September 14, 2004. Revised January 19, 2005. Accepted January 19, 2005.

The serial analysis of gene expression (SAGE) method is used to study global gene expression in cells or tissues in various experimental conditions. However, its reproducibility has not yet been definitively assessed. In this study, we have evaluated the reproducibility of the SAGE method and identified the factors that affect it. The determination coefficient (R2 ) for the reproducibility of SAGE is 0.96. However, there are some factors that can affect the reproducibility of SAGE, such as the replication of concatemers and ditags, the number of sequenced tags and double PCR amplification of ditags. Thus, corrections for these factors must be made to ensure the reproducibility and accuracy of SAGE results. A bioinformatic analysis of SAGE data is also presented in order to eliminate these artifacts. Finally, the current study shows that increasing the number of sequenced tags improves the power of the method to detect transcripts and their regulation by experimental conditions.


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