SGD^TM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

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Links to two new resources have been added to SGD: 1) GeneMANIA, a biological network integration for gene prioritization and functional prediction, and 2) the Complexome Database, a database of consensus protein complex predictions. Links to both resources have been added to the "Interactions" pull-down menu on the Locus Summary page, and to the "Interaction Resources" sections at the bottom of the Protein and Interaction pages. See Warde-Farley, et al. Nucleic Acids Res. 2010 for more information on GeneMANIA, and Benschop, et al. Molecular Cell 2010 for more information on Complexome. Thanks to Quaid Morris and Sylva Donaldson for help in setting up the GeneMANIA links and to Patrick Kemmeren for helping set up the Complexome links.

Try the beta version of YeastMine for flexible queries and fast retrieval of chromosomal features, sequences, and GO-related annotations using predefined template queries or customized queries. New datatypes and additional templates will be added in the upcoming months. YeastMine is part of a joint project with Intermine, the Rat Genome Database (RGD), and The Zebrafish Model Organism Database (ZFIN) to provide interoperability between the model organism databases via shared datatypes, such as Gene Ontology (GO) annotations or orthologs. Be a beta tester and email us your comments and questions about YeastMine.

The Gene Ontology Consortium has recently changed the format of the GO annotations file (gene_associations file, GAF) to version 2.0. The files contain two new columns (17 columns total): the Annotation Extension column and the Gene Product Form ID column. Details of format 2.0 are available at: GAF 2.0. SGD has updated the S. cerevisiae GAF to format 2.0 on its FTP site. Although SGD has not populated the two new columns with data, gene_associations file parsers/scripts could be affected by the format change.

A new 'Post-translational modifications' section has been added on the Locus Summary and Protein Info pages. This section includes links to PhosphoPep, which was previously accessible from the 'Protein Info & Structure' pull-down, and new links to PhosphoGRID, a curated database of phosphorylation sites. For more information about PhosphoGRID see Stark C, et al. (2010) PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. Database (Oxford) 2010:bap026. Thanks to Chris Stark and Mike Tyers for help in setting up the new links to PhosphoGRID.

Transcription factor DNA binding motifs determined by Badis, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87 have been added to the Locus Summary pages of 112 DNA binding proteins (for an example, see ABF2). Each binding site can be viewed in the "Regulatory Role" section of the page and is accompanied by a link to search intergenic regions in the genome for all such motifs. Thanks to Gwenael Badis-Breard, Esther Chan, Carl de Boer, and Tim Hughes for providing the data.

The Saccharomyces Genome Database (SGD^TM) project is supported by a P41 grant, National Resources [HG001315], from the National Human Genome Research Institute at the US National Institutes of Health.   The SGD^TM project is located in the Department of Genetics at the School of Medicine, Stanford University. The trademark on SGD^TM is held by The Board of Trustees, Leland Stanford Junior University.

Database Copyright © 1997-2010 The Board of Trustees, Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. How to cite SGD.