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Nat Methods. 2012 Feb 5;9(4):373-8. doi: 10.1038/nmeth.1890.

Systematic identification of gene annotation errors in the widely used yeast mutation collections.

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Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.


The baker's yeast mutation collections are extensively used genetic resources that are the basis for many genome-wide screens and new technologies. Anecdotal evidence has previously pointed to the putative existence of a neighboring gene effect (NGE) in these collections. NGE occurs when the phenotype of a strain carrying a particular perturbed gene is due to the lack of proper function of its adjacent gene. Here we performed a large-scale study of NGEs, presenting a network-based algorithm for detecting NGEs and validating software predictions using complementation experiments. We applied our approach to four datasets uncovering a similar magnitude of NGE in each (7-15%). These results have important consequences for systems biology, as the mutation collections are extensively used in almost every aspect of the field, from genetic network analysis to functional gene annotation.

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