Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

Abstract

Upon the completion of the Saccharomyces cerevisiae genomic sequence in 1996 [Goffeau,A. et al. (1997) Nature, 387, 5], several creative and ambitious projects have been initiated to explore the functions of gene products or gene expression on a genome-wide scale. To help researchers take advantage of these projects, the Saccharomyces Genome Database (SGD) has created two new tools, Function Junction and Expression Connection. Together, the tools form a central resource for querying multiple large-scale analysis projects for data about individual genes. Function Junction provides information from diverse projects that shed light on the role a gene product plays in the cell, while Expression Connection delivers information produced by the ever-increasing number of microarray projects. WWW access to SGD is available at genome-www.stanford.edu/Saccharomyces/.

FUNCTION JUNCTION

The Function Junction resource allows a Saccharomyces Genome Database (SGD) (1–3) user to simultaneously retrieve genome-wide functional analysis information from a variety of online sources for a selected gene name. The various sites surveyed by Function Junction use a wide assortment of techniques to assay or predict information about a gene product. SGD users can query all sites, or specify an interesting subset. Function Junction, which can be accessed by entering a gene or ORF name at genome-www.stanford.edu/cgi-bin/SGD/functionJunction, currently searches the following sites:

• Portal PathCalling provides data from Uetz et al. (4), investigation of protein–protein interactions and is accessible at: portal.curagen.com/extpc/com.curagen.portal.servlet.Yeast.

• UCLA Function Assignment provides the results of several different gene function prediction methods, including phylogenetic profiling, protein interactions and shared expression patterns (5–7) and can be accessed at www.doe-mbi.ucla.edu/people/marcotte/yeast.html.

• Worm–Yeast Comparison reports potential homologs identified by the Chervitz et al. sequence comparison (8) and can be found at genome-www.stanford.edu/Saccharomyces/worm/.

• Serial Analysis of Gene Expression (SAGE) provides data from the Velculescu et al. study of gene expression (9) and is available at an SGD website, genome-www.stanford.edu/Saccharomyces/SAGE/AdvancedQuery.html.

• Triples Database reports the results of transposon muta­genesis studies (10) providing data about phenotype, expression and localization and is available at ygac.med.yale.edu/triples/triples.htm.

EXPRESSION CONNECTION

Expression Connection is similar to Function Junction in concept, but it queries only microarray expression data (see Fig. 1 for an example). Using software developed at SGD, downloaded data from several microarray studies are queried to display the expression pattern of a gene and its most similarly expressed neighbors. For serial experiments, a graph showing the expression pattern over the course of the experiment is available. The datasets currently queried by Expression Connection include results of a diauxic shift timecourse (11), a sporulation time series (12), two studies of cell-cycle synchronization (13,14), a study of evolution under glucose limitation (15), a histone depletion timecourse (16), an analysis of gene expression perturbation caused by mutations in the yeast transcriptional machinery (17), an α-factor concentration series and an α-factor treatment timecourse (18). To use Expression Connection, enter a gene or ORF name at the following URL: genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl.

Figure 1.

Expression Connection. For any gene, users may display several sets of microarray data. (A) For each set of serial data, a graphic representation of the gene’s expression pattern is rendered. (B) Two color representations of the expression data are presented, showing the gene’s expression pattern along with the 20 loci whose expression patterns are most similar. The two color representations are accompanied by annotation of gene names, molecular function and biological processes.

CONCLUSIONS

Together, Function Junction and Expression Connection will serve as a central resource on the World Wide Web for quickly retrieving information generated by comprehensive analyses of the yeast genome. As more large-scale datasets are published, SGD will include them on the list of sites queried by these software packages. In this manner, SGD will enable online researchers to benefit from the accumulation of genome-wide studies of Saccharomyces cerevisiae.