ArticleNucleic acids research2016
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Large-scale genome re-annotation uncovers pathogen-specific lncRNA regulators of fungal growth and virulence.PLoS pathogens · 2026Article
- Systematic Characterization and Analysis of the Freeze-Thaw Tolerance Gene Set in the Budding Yeast,International journal of molecular sciences · 2025Article
- The transcriptional coordination of functional gene clusters is dependent on multiple chromatin remodelers in a haploid strain of the budding yeast,Frontiers in fungal biology · 2025Article
- Global analysis of the yeast knockout phenome.Science advances · 2023Article
- Functional Clustering of Metabolically Related Genes Is Conserved acrossJournal of fungi (Basel, Switzerland) · 2023Review
- Article
- Transgene insertion into the plastid genome alters expression of adjacent native chloroplast genes at the transcriptional and translational levels.Plant biotechnology journal · 2023Article
- Article
- A standard knockout procedure alters expression of adjacent loci at the translational level.Nucleic acids research · 2021Article
- Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast.Nucleic acids research · 2021Article
- Genomic Considerations for the Modification ofMicroorganisms · 2020Review
- Genomic clustering within functionally related gene families inComputational and structural biotechnology journal · 2020Review
- Article
- Cis and trans interactions between genes encoding PAF1 complex and ESCRT machinery components in yeast.Current genetics · 2018Article
- Using genetic buffering relationships identified in fission yeast to reveal susceptibilities in cells lacking hamartin or tuberin function.Biology open · 2018Article
- TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network.G3 (Bethesda, Md.) · 2017Article
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3 authors.
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No grant is acknowledged in the PubMed record.
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.
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