Integrating functional genomic information into the Saccharomyces genome database

Abstract

The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the 'locus page' and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product's cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www.stanford.edu/Saccharomyces/

Figure 1

The new locus page at SGD. This new locus page for MET16 shows how data will be organized to include several different types of information at a central location.

Figure 2

Process and function annotation of genes in a DNA microarray cluster. This cluster was originally published by Spellman et al. (5) and contains genes that are co-expressed in a cell cycle-dependent manner. The entry for MET16 is highlighted in red. The gene name, process and function are shown for each gene in the cluster (cellular component annotation has been omitted for brevity). Genes correspond to the rows, and the time points of each experiment are the columns. The colors indicate changes in gene expression in synchronized cells relative to a reference sample. Red represents increased expression, green represents decreased expression and black denotes no change. Gray areas indicate missing data points. The clustering algorithm is described by Eisen et al. (9).

Figure 3

The Gene Summary Paragraph. The Gene Summary Paragraph, shown for MET16, summarizes important findings about a particular gene. From the paragraph page, there are links to the locus pages of other relevant genes (in this case, CBF1), as well as links to additional sources of information such as the Gene Ontology controlled vocabulary terms, references and PubMed links, and the SGD Literature Guide.