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

Brian D. Peyser | Zendy; Rafael A. Irizarry | Zendy; Carol W. Tiffany | Zendy; Ou Chen | Zendy; Daniel Yuan | Zendy; Jef D. Boeke | Zendy; Forrest Spencer | Zendy

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

Author(s) -

Brian D. Peyser,

Rafael A. Irizarry,

Carol W. Tiffany,

Ou Chen,

Daniel Yuan,

Jef D. Boeke,

Forrest Spencer

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gni138

Subject(s) - biology , dna microarray , saccharomyces cerevisiae , computational biology , genetics , genome , yeast , synthetic lethality , mutant , spike (software development) , microarray , gene , gene expression , computer science , software engineering

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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