Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

Abstract

The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over the last decade. As emphasis shifts from identification of the genes to identification of the role of their gene products in the cell, SGD seeks to provide its users with annotations that will allow relationships to be made between gene products, both within Saccharomyces cerevisiae and across species. To this end, SGD is annotating genes to the Gene Ontology (GO), a structured representation of biological knowledge that can be shared across species. The GO consists of three separate ontologies describing molecular function, biological process and cellular component. The goal is to use published information to associate each characterized S.cerevisiae gene product with one or more GO terms from each of the three ontologies. To be useful, this must be done in a manner that allows accurate associations based on experimental evidence, modifications to GO when necessary, and careful documentation of the annotations through evidence codes for given citations. Reaching this goal is an ongoing process at SGD. For information on the current progress of GO annotations at SGD and other participating databases, as well as a description of each of the three ontologies, please visit the GO Consortium page at http://www.geneontology.org. SGD gene associations to GO can be found by visiting our site at http:// genome-www.stanford.edu/Saccharomyces/. ANNOTATION GOALS AND GUIDELINESThe Saccharomyces Genome Database's (SGD's) (1-5) goal of annotating yeast genes to Gene Ontology (GO) (6,7) is to provide users with accurate information about the roles of gene products in the cell and their relationship to other gene products in yeast and other organisms. The availability of published

Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms

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Predicting Subcellular Localization via Protein Motif Co-Occurrence

“…The yeast data set was generated by retrieving all proteins annotated with subcellular localization information from the Saccharomyces Genome Database (SGD; Dwight et al 2002;www. yeastgenome.org/).…”

Transitive functional annotation by shortest-path analysis of gene expression data

“…Genes were annotated by using the biological process ontology of Gene Ontology (GO) (7) provided by the Saccharomyces Genome Database (SGD) (8). To verify that genes on the same SP are likely to be involved in the same biological process, we applied our method to the Rosetta dataset and checked the results against GO-annotated biological processes in the three major cellular compartments: mitochondria, cytoplasm, and nucleus.…”