SGD Quarterly Newsletter, Fall 2009

About this newsletter:

This is the November 2009 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

Details of these items can be viewed at the SGD Blog

Take the SGD Survey

Please take our brief survey to let us know how you use SGD. The information you provide will help us prepare for our grant renewal next year.

SGD survey: http://www.yeastgenome.org/survey

SGD and the Gene Ontology's Reference Genome Project

The Gene Ontology's Reference Genome Project, begun in 2006, is a collaborative effort involving annotators from twelve reference genome groups. The primary goal is to increase the breadth and depth of annotations for sets of evolutionarily related genes across genomes to enable other genome annotation efforts to infer GO annotations for homologous genes. As part of the Reference Genome Project, SGD curators have recently completed in depth annotation of the genes in TFIID, a complex required for the formation of the preinitiation complex during RNAPII-mediated transcription. This included a review of GO and phenotype annotations, and the composition of gene summary paragraphs for subunits of this complex which include: the TATA binding protein Spt15p, as well as fourteen TBP-associated factors (TAFs): Taf1p, Taf2p, Taf3p, Taf4p, Taf5p, Taf6p, Taf7p, Taf8p, Taf9p, Taf10p, Taf11p, Taf12p, Taf13p and Taf14p.

GO Reference Genome Project: http://www.geneontology.org/GO.refgenome

Curation Focus: Mitochondrial Import

Mitochondrial import is an extremely complex, essential process involving multisubunit translocases that mediate the transit of hundreds of nuclear-encoded proteins into four different compartments of the double-membraned organelle. We have now reviewed the information available in SGD about 28 genes (MGE1, PAM16, PAM17, PAM18, SAM35, SAM37, SAM50, SSC1, TIM8, TIM9, TIM10, TIM12, TIM13, TIM17, TIM18, TIM21, TIM22, TIM23, TIM44, TIM50, TIM54, TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70) encoding proteins involved in the import process. Locus Descriptions, Gene Ontology annotations, and mutant phenotype annotations for each gene have been updated, and Gene Summary paragraphs have been added to their Locus Summary pages.

Curation Focus: Exosome, TRAMP, and SKI Complexes

The exosome is a complex that possesses 3'-5' exonuclease and endoribonucleolytic activities that are essential for diverse ribonucleolytic processes in both the nucleus and the cytoplasm. The nuclear exosome is associated with the TRAMP complex while the cytoplasmic exosome is assocated with Ski7p and the SKI complex. Information in SGD about the 21 genes (CSL4, RRP4, RRP40, SKI6, RRP42, RRP43, RRP45, RRP46, MTR3, DIS3, RRP6, LRP1, MPP6, PAP2, TRF5, MTR4, AIR1, AIR2, SKI2, SKI3 and SKI8) encoding the subunits of the exosome, TRAMP, and SKI complexes has recently been reviewed and updated, including their descriptions, GO annotations, and mutant phenotypes, and Gene Summary Paragraphs have been added to their Locus Summary pages.

YeastGFP data available from YeastRC and SGD

Images of the GFP fusion proteins described in Huh WK et al (2003) Nature 425:686 are now being hosted by the Yeast Resource Center (YeastRC, Seattle). They can be accessed via the Localization Resources pull-down on the right hand side of SGD Locus Summary pages. Select the 'YeastRC Localization (Seattle)' option and follow the View Data hyperlink on the YeastRC page. Thanks to Trisha Davis, Michael Riffle and the Yeast RC for adding the data and help in setting up these links.

YeastRC: http://www.yeastrc.org/pdr/pages/front.jsp

In addition, SGD is now hosting the YeastGFP database of global analysis of protein localization studies in the budding yeast, S. cerevisiae, originally designed and built by the laboratories of Erin O'Shea and Jonathan Weissman at the University of California, San Francisco. Links to individual ORFs are available from the Localization Resources pull-down on the right hand side of SGD Locus Summary pages. Select the 'YeastGFP DB (UCSF) at SGD' option. Thanks to Jonathan Weissman and Nick Ingolia for providing the software and files.

YeastGFP at SGD: http://yeastgfp.yeastgenome.org/

Enhancements to GO Term Finder

SGD has included two new options in the GO Term Finder, a tool for finding significant GO terms shared among a list of genes.

• Name your analysis/search: allows naming of searches in order to keep track of results when performing multiple GO Term Finder analyses.
• Calculate the False Discovery Rate (FDR): calculates the FDR for each term, indicating the expected proportion of false positives among the set of significant results.

GO Term Finder: http://www.yeastgenome.org/TermFinder

Yeast Go Slims updated

The Yeast GO Slims are sets of high-level GO terms that best represent the major biological processes, molecular functions, and cellular components that are found in S. cerevisiae. GO Slim terms are useful in mapping precise, "granular" gene annotations to more general "high-level" terms. These terms have been selected by SGD curators based on annotation statistics and biological significance. Recently, SGD curators reviewed the Yeast GO Slim terms and made necessary updates to the Process set, including the addition of seven new terms. No changes were made to the Function and Component sets of slim terms.

The Yeast GO Slims are available for analysis via the GO Slim Mapper tool and the Advanced Search tool. Mapping of all the yeast gene products to the Yeast GO Slims is also available as a graphical view on the Genome Snapshot page and via the go_slim_mapping.tab file on the FTP site.

GO Slim Mapper: http://www.yeastgenome.org/SlimMapper

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 58 features.

Genes with new summary paragraphs are reported weekly on SGD's "What's New" page: http://www.yeastgenome.org/whats_new.shtml

Community News

• Job opportunities in yeast labs: http://wiki.yeastgenome.org/index.php/Positions_in_yeast_labs

• Reactome Pathway Database User Survey: Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, they are actively soliciting comments from the research community in order to assess community needs. They are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that they can continue to improve the Reactome site and tools.

• Links to Cyclebase have been added to the "Functional Analysis" pull-down on the right hand side of SGD Locus Summary pages. This resource provides a web interface for visualization, multi-species comparison, and download of genome-wide cell-cycle data and analysis result. Thanks to Lars Juhl Jensen for helping set up these links.

Cyclebase: http://cyclebase.org

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 & Molecular Biology Meeting

Vancouver, BC, Canada

July 27 - August 1, 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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