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.
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Peyser
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
authors.forename: Carol W
authors.initials: CW
authors.lastname: Tiffany
authors.forename: Ou
authors.initials: O
authors.lastname: Chen
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Yuan
authors.forename: Jef D
authors.initials: JD
authors.lastname: Boeke
authors.forename: Forrest A
authors.initials: FA
authors.lastname: Spencer
mesh_terms: D003627:Data Interpretation, Statistical; D005456:Fluorescent Dyes; D005804:Genes, Lethal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017384:Sequence Deletion; D016324:Sequence Tagged Sites
chemical_list: D005456:Fluorescent Dyes