Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae.

Abstract

The yeast mutant collections are a fundamental tool in deciphering genomic organization and function. Over the last decade, they have been used for the systematic exploration of ∼6 000 000 double gene mutants, identifying and cataloging genetic interactions among them. Here we studied the extent to which these data are prone to neighboring gene effects (NGEs), a phenomenon by which the deletion of a gene affects the expression of adjacent genes along the genome. Analyzing ∼90,000 negative genetic interactions observed to date, we found that more than 10% of them are incorrectly annotated due to NGEs. We developed a novel algorithm, GINGER, to identify and correct erroneous interaction annotations. We validated the algorithm using a comparative analysis of interactions from Schizosaccharomyces pombe. We further showed that our predictions are significantly more concordant with diverse biological data compared to their mis-annotated counterparts. Our work uncovered about 9500 new genetic interactions in yeast.

DOI: 10.1093/nar/gkv1284

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Cite this paper

@article{Atias2016SystematicIA, title={Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae.}, author={Nir Atias and Martin Kupiec and Roded Sharan}, journal={Nucleic acids research}, year={2016}, volume={44 5}, pages={e50} }