A website to identify shared genes in Saccharomyces cerevisiae homozygous deletion library screens

• Main Author: Mark D. Temple
• Format: Article
• Language: English
• Published: BMC 2018-05-01
• Series: BMC Bioinformatics
• Subjects: Yeast; Saccharomyces cerevisiae; Database; Deletion library; Venn intersection
• Online Access: http://link.springer.com/article/10.1186/s12859-018-2212-4
• ISSN: 1471-2105

Abstract Background The homozygous yeast deletion library includes approximately 4800 diploid strains each containing one deleted non-essential gene. Hundreds of publications have arisen through experimentation using this genome-wide biological resource. As part of this work over 677 genesets have been collated from these experiments representing the phenotypic responses of the library to a diverse set of chemical and physical challenges. Description A website called the Saccharomyces cerevisiae Homozygous Deletion Library Tools (ScHo DeLiTo-96) has been developed with the primary goal of browsing and identifying genes shared between these responsive phenotypes (available at yeastdb.org). Geneset comparisons have been performed for each phenotype against all others to identify common genes. Genesets and other curated information are stored in a relational database and a website interface allows users to query and browse the data in an intuitive way to reveal commonality between selected phenotypic responses. The most commonly occurring genes in all of the stored phenotypes are highly over-represented in the GO slim term “cellular ion homeostasis” indicating that genes shared between phenotypes may highlight a common cellular response. Additionally, user derived genesets can be uploaded and intersected against the stored data to reveal common responses which may otherwise have been obscure. Conclusion These tools provide a simple method to perform niche enquiries between datasets derived from the yeast deletion library.