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.

A memorial symposium to remember Dr. Elizabeth W. Jones and her contributions will be held at Carnegie Mellon University on Wednesday, October 15, 2008 at 4:00 p.m. David Botstein, Peter Bruns, Christine Guthrie, and Aaron Mitchell will speak. We invite you to join us for the memorial symposium and reception. Additional details will be made available on Carnegie Mellon's Department of Biological Sciences website: http://www.cmu.edu/bio/. Please R.S.V.P. at this web page: http://www.bio.cmu.edu/symposiumRSVP.php. - John Woolford

SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

• Genome Snapshot
• New papers added to SGD this week.
• View Genome-wide Analysis papers in SGD.
• Do a literature search.
• Table of Gene Summary Paragraphs (new ones highlighted yellow).

SGD has incorporated computational GO annotations from the functional predictions based on the analysis of multiple high-throughput datasets published in Huttenhower and Troyanskaya, 2008. This method is described further in Myers et al., 2005, Myers et al., 2007, and Huttenhower et al., 2006. These data can be viewed in the computational GO annotation section (for example, see GO annotations for YDL156W). Thanks to Curtis Huttenhower and Olga Troyanskaya for working with SGD on incorporating these data.

SGD has incorporated computational GO annotations from a method published in Tian et. al., Genome Biology 2008 that combines guilt-by-profiling and guilt-by-association analysis to infer gene function. These data can be viewed in the computational GO annotation section (for example, see GO annotations for YCR041W). Links to gene pages at the YeastFunc viewer are available on the GO Annotation details page in the 'Assigned By' column and in the 'Functional Analysis' pull-down on the right hand side of the Locus Summary pages. Thanks to Weidong Tian, John Beaver, and Fritz Roth for working with SGD on incorporating these data and links.

The SGD Quick Search has been expanded to retrieve information from 14 major categories including: names, descriptions, functional information, phenotype data, colleagues, authors, and external IDs. Results are now organized under topic headings that group similar types of information. This basic search is accessible from the top of most SGD pages, as well as from the Search Options page.

The Interactions page has been updated to allow physical and genetic interactions to be sorted and filtered based on an experimental method, reference, or phenotype. This table also includes notes about the interaction as well as the annotation type to facilitate the identification of high-throughput datasets. SGD now includes 121,580 curated physical and genetic interactions from the BioGRID version 2.0.42 release. New interactions are added on a monthly basis. These data are available over the web and via bulk download through both BioGRID and a new FTP file at SGD.

SGD is now releasing our improved and expanded mutant phenotype pages. Over the past year, we re-curated existing mutant phenotypes and added more phenotype data, both using a new controlled-vocabulary system. The implementation of this system greatly increases the amount of detailed information that can be captured for each phenotype, and facilitates searching and comparison of mutant phenotypes. A brief version of the phenotype is displayed on the Locus Summary page for each gene, and the complete information is accessible via the 'Phenotype' tab at the top of the page (for example, see WHI3). [More...]

SGD curators periodically update the systematic sequence and its annotation. Information regarding changes can be found via the Summary of Chromosome Sequence and Annotation Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2008-06-02 and 2008-06-06, the sequences of Chromosomes IV, X, and XI were updated, affecting ORFs YDL038C, PRM7/YDL039C, BUD4/YJR092W, and ASK1/YKL052C; the annotation of ORFs LSB3/YFR024C-A, and ADH4/YGL256W on Chromosomes VI and VII were udpated; and a new LTR YCLWdelta15 was annotated on Chromosome III.

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 © 1997-2008 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.