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

doi:10.1093/nar/gni138

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

School of Medicine

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

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 language	English (US)
Pages (from-to)	1-5
Number of pages	5
Journal	Nucleic acids research
Volume	33
Issue number	16
DOIs	https://doi.org/10.1093/nar/gni138
State	Published - 2005

ASJC Scopus subject areas

Genetics

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10.1093/nar/gni138

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title = "Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools",

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.",

author = "Peyser, {Brian D.} and Irizarry, {Rafael A.} and Tiffany, {Carol W.} and Ou Chen and Yuan, {Daniel S.} and Boeke, {Jef D.} and Spencer, {Forrest A.}",

note = "Funding Information: The authors thank Z. Wu, X. Pan, J. Bader and colleagues from our laboratories for stimulating discussions. This work was supported by NIH HG02432 to J.B., R.I. and F.S. which also funded the Open Access publication charges for this article.",

year = "2005",

doi = "10.1093/nar/gni138",

language = "English (US)",

volume = "33",

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journal = "Nucleic acids research",

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T1 - Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools

AU - Peyser, Brian D.

AU - Irizarry, Rafael A.

AU - Tiffany, Carol W.

AU - Chen, Ou

AU - Yuan, Daniel S.

AU - Boeke, Jef D.

AU - Spencer, Forrest A.

N1 - Funding Information: The authors thank Z. Wu, X. Pan, J. Bader and colleagues from our laboratories for stimulating discussions. This work was supported by NIH HG02432 to J.B., R.I. and F.S. which also funded the Open Access publication charges for this article.

PY - 2005

Y1 - 2005

N2 - 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.

AB - 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.

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

Abstract

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