SGD Quarterly Newsletter, Summer 2005

About this newsletter:

This is the July 2005 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.

Other relevant URLs mentioned in this newsletter are also at the bottom of the page. As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Navigation tabs

Navigation tabs have been added in order to provide easier access to different types of information currently available for genes and chromosomal features. These tabs are hyperlinked to pages already accessible via pull-down options on the right hand side of a Locus Page. A colored tab indicates the page being viewed. The navigation tabs can be found at the top of the following pages: Locus Page, Locus History, Literature Guide, Gene Ontology evidence and references, Phenotype details and references, Interaction details and references, Expression Summary, and Protein Info.

Primer sequences

Primer sequences previously distributed by Invitrogen/Research Genetics have been remapped to the current S. cerevisiae genome sequence and added to the GBrowse map viewer. Information about individual primer sequences as well as predicted PCR products from unique primer pairs can be viewed as tracks in Gbrowse. In addition, the GFF file for these primers and PCR products is available from the ftp site.

A new microarray data set

A new microarray data set, "Exploration of essential gene functions via titratable promoter alleles" (Mnaimneh, S., et al. (2004)) has been added to Expression Connection. This study measures expression of each S. cerevisiae gene under depletion conditions for each of 215 essential gene products. Thanks to Tim Hughes for assistance with this data set. The Expression Connection tool allows users to search and compare expression patterns across multiple microarray experiments. A summary of expression changes for an individual ORF can be viewed by selecting "Expression Connection Summary" from the Functional Analysis pull-down located on the right hand side of the Locus Page or clicking on the histogram. Data sets in Expression Connection are also available for download from the SGD ftp site.

New gene summary paragraphs for 36 genes involved in N-linked glycosylation

Summary Paragraphs have been added to 36 genes involved in N-linked glycosylation, many of which are homologous to genes implicated in human congenital disorders of glycosylation. The paragraphs highlight in a concise form the most important findings about genes and their functions. To see examples, visit the ALG7, OST3, and GFA1 Locus Pages.

Large scale phenotype data added

Several large scale datasets have been added over the last months. They include the studies of a chitin synthesis network (Lesage, G., et al., BMC Genet. 2005 Feb 16;6(1):8), mechanisms of haploinsufficiency (Deutschbauer, A.M., et al., Genetics. 2005 Apr;169(4):1915-25), glycogen accumulation defects (Wilson, W.A., et al., Mol Cell Proteomics. 2002 Mar;1(3):232-42) and TOR function and rapamycin responses (Xie, M.W., et al., Proc Natl Acad Sci U S A. 2005 May 17;102(20):7215-20).

Deletion strain barcode arrays now available

Jef Boeke's lab, in collaboration with others, designed a microarray based on the tags (or barcodes) used to uniquely identify the individual mutant strains in the yeast knockout collection; these arrays have been used successfully by the SLAM (Synthetic Lethality Analyzed by Microarray) project. Because these arrays will likely be generally useful to the research community for a variety of other types of experiments, a buyer's consortium has been established to enable researchers to purchase the arrays through Agilent Technologies; academic researchers will receive a special discount. Please note that neither the SLAM project, its scientists, nor members of the consortium receive compensation of any kind as a result of sales of these arrays. To join the consortium, go to the barcode home page; for more information (e.g. protocols, materials, etc) about these arrays, see the SLAM home page at Johns Hopkins University.

Bratislava abstracts available online

Abstracts of the XXIIth International Conference on Yeast Genetics and Molecular Biology to be held in on August 7 - 12 in Bratislava, Slovakia are available in advance of the meeting. All abstracts can be queried via an online search form available at SGD.

Community News

• CryptoBase: A scientific database resource for the genome of C. neoformans var. grubii (serotype A), an opportunistic yeast pathogen of humans; built and maintained at UCSF.
• Addgene: Repository and distributor of plasmid constructs described in published literature.

Upcoming conferences

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

• August 7 - August 12, 2005 XXII International Conference on Yeast

Genetics and Molecular Biology INCHEBA Exhibition & Fair Center,

Bratislava, Slovak Republic

• August 16 - August 21, 2005, Yeast Cell Biology, Cold Spring Harbor

Laboratory, Cold Spring Harbor, NY

• September 14 - September 18, 2005, The Sixth International Conference on AAA Proteins Schloss Seggau, Southern Styria, Austria

• October 28 - November 1, 2005, Genome Informatics

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

• November 12 - November 17, 2005, Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi

Sant Feliu de Guixols, Spain

• November 13 - November 17, 2005, 4th International Meeting on Yeast and Apoptosis

Wyndham Miami Beach Resort, Miami, FL

• January 5 - January 7, 2006, Genetic Analysis: Model Organisms to Human Biology

San Diego, California

• July 25 - July 30, 2006, Yeast Genetics and Molecular Biology Meeting

Princeton University, Princeton, NJ

• July 1 - July 6, 2007, 23rd International Conference on Yeast Genetics and Molecular Biology

Melbourne, Australia

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