title: 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.
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
authors.forename: Nir
authors.initials: N
authors.lastname: Atias
authors.affiliation: Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel martin@post.tau.ac.il.
authors.forename: Martin
authors.initials: M
authors.lastname: Kupiec
authors.affiliation: Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel roded@post.tau.ac.il.
authors.forename: Roded
authors.initials: R
authors.lastname: Sharan
mesh_terms: D000465:Algorithms; D004843:Epistasis, Genetic; D063990:Gene Ontology; D005800:Genes, Fungal; D023281:Genomics; D058977:Molecular Sequence Annotation / Q000379:methods*; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics / Q000378:metabolism