SGD Quarterly Newsletter, Summer 2010

About this newsletter:

This is the Summer 2010 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can also subscribe to SGD's RSS feed to receive updates on SGD news: http://www.yeastgenome.org/feed

Come see us at YGM

SGD representatives will be attending the 2010 Yeast Genetics & Molecular Biology Meeting in Vancouver next week. We will present two posters and participate in a workshop ("SGD, other databases and computational tools") on Saturday afternoon. Please come by, say hello, complete our survey, and let us know how you use SGD. We would love to see you!

Beta release of YeastMine

Try the beta version of YeastMine for flexible queries and fast retrieval of chromosomal features, sequences, interactions, and GO- and phenotype-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.

Try YeastMine at: http://yeastmine.yeastgenome.org:8080/yeastmine/

Additional DNA binding site motifs available

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.

Resources for post-translational modifications

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.

New Resource links

Links to two new resources have been added to SGD:

1. GeneMANIA, a biological network integration for gene prioritization and functional prediction
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. (2010) Nucleic Acids Res. 38 Suppl:W214-20 for more information on GeneMANIA, and Benschop, et al. (2010) Molecular Cell 38(6):916-928 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.

New file format for SGD's GO annotations file

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. 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.

Details of format 2.0 are available at: http://www.geneontology.org/GO.format.gaf-2_0.shtml

New Gene Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, and are designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. During the last quarter new summary paragraphs have been added to their respective Locus Summary pages for 74 features. Genes with new summary paragraphs are reported weekly on SGD's What's New page.

Upcoming Conferences and Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

• Yeast Genetics and Molecular Biology Meeting

Vancouver, Canada

July 27 - August 1, 2010

• Society for Industrial Microbiology 60th Annual Meeting

San Francisco, California

August 1-5, 2010

• Systems Biology: Networks

Hinxton, UK

August 11-15, 2010

• Genome Informatics

Hinxton, UK

September 15-19, 2010

• International Yeast Model Convention 2010, a tribute to Piotr Slonimski

Rome, Italy

September 22-25, 2010

• 28th SMYTE (Small Meeting on Yeast Transport and Energetics)

Heritage Village, Manesar, Gurgaon, India

September 23-27, 2010

• EMBO Experimental Approaches to Evolution and Ecology using Yeast

Heidelberg, Germany

September 29 - October 3, 2010

• XV International Conference on Yeast Genetics and Molecular Biology

Olsztyn, Poland

July 11-16, 2011

asterisks indicate attendance by SGD.*

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