title: Saccharomyces genome database provides new regulation data.
abstract: The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regulatory information to SGD and present it on a new tabbed section of the Locus Summary entitled 'Regulation'. We are compiling transcriptional regulator-target gene relationships, which are curated from the literature at SGD or imported, with permission, from the YEASTRACT database. For nearly every S. cerevisiae gene, the Regulation page displays a table of annotations showing the regulators of that gene, and a graphical visualization of its regulatory network. For genes whose products act as transcription factors, the Regulation page also shows a table of their target genes, accompanied by a Gene Ontology enrichment analysis of the biological processes in which those genes participate. We additionally synthesize information from the literature for each transcription factor in a free-text Regulation Summary, and provide other information relevant to its regulatory function, such as DNA binding site motifs and protein domains. All of the regulation data are available for querying, analysis and download via YeastMine, the InterMine-based data warehouse system in use at SGD.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Maria C
authors.initials: MC
authors.lastname: Costanzo
authors.forename: Stacia R
authors.initials: SR
authors.lastname: Engel
authors.forename: Edith D
authors.initials: ED
authors.lastname: Wong
authors.forename: Paul
authors.initials: P
authors.lastname: Lloyd
authors.forename: Kalpana
authors.initials: K
authors.lastname: Karra
authors.forename: Esther T
authors.initials: ET
authors.lastname: Chan
authors.forename: Shuai
authors.initials: S
authors.lastname: Weng
authors.forename: Kelley M
authors.initials: KM
authors.lastname: Paskov
authors.forename: Greg R
authors.initials: GR
authors.lastname: Roe
authors.forename: Gail
authors.initials: G
authors.lastname: Binkley
authors.forename: Benjamin C
authors.initials: BC
authors.lastname: Hitz
authors.forename: J Michael
authors.initials: JM
authors.lastname: Cherry
mesh_terms: D001665:Binding Sites; D030541:Databases, Genetic; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D016681:Genome, Fungal; D020407:Internet; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors