SGD Quarterly Newsletter, Winter 2005

About this newsletter:

This is the January 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

References for information on Locus Page

The Locus Page has been updated to display the references that have been used as citations for the Description, Name Description, and Gene Product. If references are available, a 'View References' link will be displayed on top of the locus pages and a citation number will be listed after the information. These references, along with the references used in the Summary Paragraph, are listed at the bottom of the Locus page.

New features added to Advanced Search tool

The Advanced Search tool (previously called "Chromosomal Features Search") provides an easy way to generate lists of genes based on a variety of criteria. For example, you can retrieve all genes known to be involved in meiosis, all mitochondrial proteins within a certain molecular weight, all uncharacterized ORFs, etc. We recently added new search options to this tool, including interaction and expression data as well as open reading frame classifications (Dubious, Verified, Uncharacterized).

Files for computational predictions available

Results from two studies ( Troyanskaya et al. (2003) PNAS 100:8348-53 and Lee et al. (2004) Science 306:1555-8) that predict functional interactions between genes have been added to the SGD ftp site.

SGD's paper in 2005 NAR Database Issue

The 2005 Nucleic Acids Research Database issue is now available. This issue includes a paper by the SGD staff describing the following new tools at SGD:

• Fungal BLAST (for nucleotide and protein searches against fungal sequences available at GenBank)
• Model Organism BLASTP Best Hits (for links to curated information about sequences conserved in other organisms)

New options for Batch Download Tool

The Batch Download Tool has been updated so that Gene Ontology (GO) annotations can be downloaded for a list of standard gene names or systematic names. The GO annotations can be downloaded simultaneously with DNA sequences, protein sequences, and chromosomal coordinate information for the same list of gene games or systematic names. In addition, links to view "Flanking Features" have been added to the "Maps & Displays" pull-down menu on the Locus Page and Gene/Sequence Resources so that neighboring chromosomal features can be viewed and downloaded.

New features on Locus Page

Several new links and features have been added to the Locus Page:

An "Expression Summary" histogram summarizes the number of microarray experiments (samples) in which the expression changed for that ORF. This histogram can be found in the lower right hand corner of the Locus Page under the "Functional Analysis" pull-down menu. It is a hyperlink to the Expression Connection summary page.

Links to view ATCC/WashU Clones in Gbrowse are available from the "Maps & Displays" pull-down menu.

Links to GPM DB, a database summarizing mass spec data, are available from the "Protein Info & Structure" pull-down menu. Thanks to Ron Beavis for helping set up the links.

Expansion of our literature search

In response to comments received in the SGD survey taken at the YGM meeting this summer, SGD is in the process of expanding its literature search to add more relevant papers to the database. As a result, you may notice more references in the Literature Guide of the Locus Pages. We are in the process of curating these new references and deleting any that are not relevant. Please feel free to alert us to any problems that you notice.

Information about lab strain backgrounds

SGD has created a Lab Strains summary page describing strains commonly used by yeast researchers, such as S288C, SK1, Sigma 1278B and W303. We will continue to add information on genotypes and important phenotypes for these backgrounds and others. If you have information that should be included, please send an e-mail with the information and a reference, if possible, to yeast-curator@genome.stanford.edu.

Coming Soon: Genome Snapshot

In response to our users' requests, we are creating a web display to show an overview of the state of the genome, a Genome Snapshot. This page will summarize the status of the genome and will be updated in real time based on the existing data. A graphical view will show the distribution of ORFs by status: Verified, Uncharacterized, or Dubious. A table will show the number of each type of feature (Verified ORFs, tRNA, ARS, etc.) present on each chromosome. Bar charts will show the distribution of genes annotated to a set of high level GO terms. We will make an announcement on our home page when the Genome Snapshot becomes available.

Community News

• March 12 - March 18, 2005 FEBS Advanced Lecture Course on Systems

Biology: From Molecules and Modelling to Cells, Gosau, Austria

• March 15 - March 20, 2005 Twenty Third Fungal Genetics Conference,

Asilomar Conference Center, Pacific Grove, CA

• May 11 - May 15, 2005 The Biology of Genomes, Cold Spring Harbor

Laboratory, Cold Spring Harbor, NY

• May 12 - May 14, 2005 Seventh International Yeast Lipid Conference,

University of Wales Swansea, UK

• May 21 - May 28, 2005 FEBS Advanced Lecture Course on Human Fungal

Pathogens: Molecular Mechanisms of Host-Pathogen Interactions and

Virulence, La Colle sur Loup, France

• 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

• October 26 - October 30, 2005, Genome Informatics, Cold Spring

Harbor Laboratory, Cold Spring Harbor, NY

Relevant URLs

For What's New items:

1. SGD's paper in 2005 NAR Database Issue http://nar.oupjournals.org/cgi/content/full/33/suppl_1/D374?ijkey=81BD5zIUk6RQQ&keytype=ref

2. Information about lab strain backgrounds http://www.yeastgenome.org/straintable.shtml

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