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

Brian D. Peyser, Rafael A. Irizarry, Carol W. Tiffany, Ou Chen, Daniel S. Yuan, Jef D. Boeke, Forrest A. Spencer

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1-5
Number of pages5
JournalNucleic Acids Research
Volume33
Issue number16
DOIs
StatePublished - 2005

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Saccharomycetales
Yeasts
Genome
Sequence Deletion
Oligonucleotides
Saccharomyces cerevisiae
Color
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Peyser, B. D., Irizarry, R. A., Tiffany, C. W., Chen, O., Yuan, D. S., Boeke, J. D., & Spencer, F. A. (2005). Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Research, 33(16), 1-5. DOI: 10.1093/nar/gni138

Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. / Peyser, Brian D.; Irizarry, Rafael A.; Tiffany, Carol W.; Chen, Ou; Yuan, Daniel S.; Boeke, Jef D.; Spencer, Forrest A.

In: Nucleic Acids Research, Vol. 33, No. 16, 2005, p. 1-5.

Research output: Contribution to journalArticle

Peyser, BD, Irizarry, RA, Tiffany, CW, Chen, O, Yuan, DS, Boeke, JD & Spencer, FA 2005, 'Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools' Nucleic Acids Research, vol 33, no. 16, pp. 1-5. DOI: 10.1093/nar/gni138

Peyser, Brian D.; Irizarry, Rafael A.; Tiffany, Carol W.; Chen, Ou; Yuan, Daniel S.; Boeke, Jef D.; Spencer, Forrest A. / Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.

In: Nucleic Acids Research, Vol. 33, No. 16, 2005, p. 1-5.

Research output: Contribution to journalArticle

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