Saccharomyces genome database informs human biology

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.

Figure 1.

The top portion of the YeastMine homepage (https://yeastmine.yeastgenome.org/). The Homology tab is selected and the Gene → Functional Complementation template query is indicated by the pink rectangle. Selecting this query brings up the Gene → Functional Complementation query page shown in Figure 2.

Figure 2.

A portion of the Gene → Functional Complementation query page in YeastMine. Entering a yeast gene or a list of yeast genes retrieves human genes that show functional complementation. Currently, only data for yeast and human genes are available.

Figure 3.

Sample of disease-relevant, functionally complemented yeast genes from the top 3 enriched GO terms in Table 2. Mutations in each of the yeast genes shown are either fully or partially complemented by their respective human homolog, indicated on the right. Diseases associations for the complementing human genes were taken from the Online Mendelian Inheritance in Man (OMIM; https://www.omim.org/; 8), a catalog of human genes and genetic disorders.

Figure 4.

Example search results for ‘mitotic cell cycle’ at SGD (https://yeastgenome.org/). Only the first two results are shown. Multiple categories, or ‘facets’, are displayed on the left side of the page to enable filtering and refining of search results. Additional facets are available within each category and appear once a category is selected.