Global analysis of the yeast knockout phenome

Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae, enabled by its knockout collection, have produced the largest, richest, and most systematic phenotypic description of any organism. However, integrative analyses of this rich data source have been virtually impossible because of the lack of a central data repository and consistent metadata annotations. Here, we describe the aggregation, harmonization, and analysis of similar to 14,500 yeast knockout screens, which we call Yeast Phenome. Using this unique dataset, we characterized two unknown genes (YHR045W and YGL117W) and showed that tryptophan starvation is a byproduct of many chemical treatments. Furthermore, we uncovered an exponential relationship between phenotypic similarity and intergenic distance, which suggests that gene positions in both yeast and human genomes are optimized for function.

Automated summary

Genome-wide phenotypic screens in Saccharomyces cerevisiae have provided the most comprehensive description of any organism, but data integration has been hindered by lack of a central repository. In this study, we aggregated and analyzed around 14,500 yeast knockout screens, creating the Yeast Phenome dataset. Using this dataset, we identified two unknown genes and discovered a relationship between phenotypic similarity and intergenic distance, suggesting gene optimization in yeast and human genomes.