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Nucleic Acids Research 2005 33(16):e140; doi:10.1093/nar/gni138
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Published online 15 September 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}oxfordjournals.org

Methods Online

Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools

Brian D. Peyser1,3, Rafael A. Irizarry2, Carol W. Tiffany1, Ou Chen1, Daniel S. Yuan3, Jef D. Boeke3 and Forrest A. Spencer1,3,*

1McKusick-Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University Baltimore, MD, USA 2Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA 3Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University Baltimore, MD, USA

*To whom correspondence should be addressed. Tel: +1 011 410 614 2536; Fax: +1 011 410 614 8600; Email: fspencer{at}jhmi.edu

Received April 11, 2005. Revised June 24, 2005. Accepted August 26, 2005.

Saccharomyces cerevisiae knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. TAG arrays report abundance of unique oligonucleotide ‘TAG’ sequences incorporated into each deletion mutation of the yeast knockout collection, allowing measurement of relative strain representation across experimental conditions for all knockout mutants simultaneously. One application of TAG arrays is to perform genome-wide synthetic lethality screens, known as synthetic lethality analyzed by microarray (SLAM). We designed a fully defined spike-in pool to resemble typical SLAM experiments and performed TAG microarray hybridizations. We describe a method for analyzing two-color array data to efficiently measure the differential knockout strain representation across two experimental conditions, and use the spike-in pool to show that the sensitivity and specificity of this method exceed typical current approaches.

Correspondence may also be addressed to Rafael A. Irizarry, Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, 615 N Wolfe Street E3620, Baltimore, MD 21205, USA. Email: rafa{at}jhu.edu


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