Gene Ontology annotations at SGD: new data sources and annotation methods

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current.

Exploring transcription regulation through cell-to-cell variability

“…Of these, 148 genes have both an extreme mean and variability phenotype. To understand whether the phenotypes highlight different cellular functions, we tested for GO categories and protein complexes (19,20) that are enriched with genes in either phenotype. From 1,337 distinct gene sets we examined (Materials and Methods), 50 categories were significantly enriched in genes with a mean phenotype and 50 categories with variability phenotype (Dataset S1).…”

Budding YeastSSD1-VRegulates Transcript Levels of Many Longevity Genes and Extends Chronological Life Span in Purified Quiescent Cells

“…Systematic global screens have identified ϳ200 genes that show genetic or physical interactions with Ssd1 (Reguly et al, 2006). These genes show a striking enrichment (Hong et al, 2008) for posttranslational modifiers (p ϭ 10 Ϫ14 ), including 19 kinases and nine histone deacetylases, and genes involved in the cell cycle and cell morphogenesis (p ϭ 10 Ϫ8 ). ssd1 mutants display sensitivity to high osmolarity, caffeine, fungicides¤ and numerous other compounds, which suggests a role for this protein in the maintenance of cell wall integrity (Ibeas et al, 2001;Parsons et al, 2004), but its mechanism of action remains obscure.…”

Industrial systems biology

“…A close inspection of Table II reveals that combined, all of the metabolic reconstructed networks have an average genome coverage of 14.6 AE 8.1% (n ¼ 29). If S. cerevisiae, the most well-characterized eukaryote, is isolated as an example, the most recent metabolic reconstructed network has genome coverage of 13.6%, while 4,691 of the 6,608 total ORFs, 70.9%, have a verified function (Fisk et al, 2006;Hong et al, 2008). From a more general perspective, the problem of metabolic gap closing is exacerbated by the relatively large orphan metabolic activities, where 30-40% of the known metabolic activities that are classified by the Enzyme Commission have no associated genomic sequences in any organism (Breitling et al, 2008;Green and Karp, 2005;Lespinet and Labedan, 2006).…”