SGD Quarterly Newsletter, Spring 2003

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About this newsletter:

This is the April 2003 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.

As always, please contact SGD with any comments or suggestions at:

New SGD Features

New Version of Expression Connection: SGD has released a new version of Expression Connection that provides 3 different types of searches and makes it possible to search data for more than one gene name at a time. The different searches include:

  1. Search multiple datasets for expression results using one or more gene names.
  2. Find datasets where the expression of one or more genes changes by an amount you define.
  3. Find all genes that change expression in a manner you define in one or more datasets.

In addition to the added searches, results from multiple datasets are now presented in a succinct tabular form. Pearson Correlation and Expression Graphs are also displayed for each queried gene.

Chromosomal Features Search: The Chromosomal Features Search is a new Advanced Search that allows one to easily retrieve desired chromosomal features (ORFs, tRNAs, centromeres, etc). One can either retrieve all chromosomal features of a certain type or limit results based on selected criteria (such as molecular weight, amino acid length, or broad categories of function, process, or cellular location). In addition, results can be downloaded as a text file.

New Links on SGD locus pages: Links to outside sources for specialized information on a gene have been added to the SGD locus pages. This allows one to go directly to relevant information for a gene of interest as provided by the outside resource. Locus pages now include links to the Database of Interacting Proteins (DIP), the Biomolecular Interaction Network Database (BIND), the SCOP Superfamily website, BLASTP results at NCBI, and the Open Biosystems mutant strain order form. All these links on the locus page lead to information in the external database specific to the relevant gene or ORF. We would like to thank Lukasz Salwinski (DIP), Julian Gough (SCOP Superfamily), and Bob Burruss (Open Biosystems) for helping us set up these links.

Phenotype data from Steinmetz et al.: SGD has added two new classes of mutants to its phenotype section based on the data from Steinmetz et al. (Steinmetz LM, et al. (2002) Systematic screen for human disease genes in yeast. Nat Genet 31(4):400-4). These include "growth defect on a non-fermentable carbon source" and "growth defect on a fermentable carbon source." If a gene exhibits either of these phenotypes, the relevant phenotype will be displayed in the Phenotype section of its locus page.

Table of Community Annotations: In February of this year, SGD introduced a Community Annotation tool, which allows researchers to submit one or more "Research Highlights," each describing a published result about a given gene. The Table of Community Annotations lists genes and ORFs that have community annotations as well as the topic categories for these annotations and their contributors.

Community News

Information on registration and abstract deadlines for the following conferences is available at:

  • The Cold Spring Harbor Yeast Cell Biology meeting will be held from
August 12-17, 2003. Abstracts are due May 21, 2003.
  • The International Meeting on Yeast Apoptosis will be held at the
Smolenice castle, Slovak Republic, September 17-20, 2003. Abstracts
are due May 31, 2003.
  • The XXI International Conference on Yeast Genetics and Molecular
Biology will be held in Goteborg, Sweden, July 7-12, 2003.

Other SGD News

Community Annotation t-shirt contest: This is your chance to get one of the "Superbud" T-shirts modeled by SGD at last summer's Yeast Genetics and Molecular Biology Meeting in Madison, Wisconsin. During the next 3 months, SGD will award "Superbud" T-shirts to 75 researchers (25/month, randomly selected) who contribute community annotations to our site (limit 1 shirt/researcher).

Expired Gene Name Reminder: If you have received an e-mail from us regarding an expired gene name reservation, please take a moment to let us know the status of publication for this gene name so it can be determined whether or not the gene name reservation should be extended. The easiest way to update this information is to use our Gene Registry Form, selecting "Update existing information" at the top

Webminer: In March, 2003, SGD began hosting Webminer, developed by Max Heiman while at UCSF. Webminer is a tool that allows one to select specific experiments from one or more expression datasets, specify parameters for searching the dataset(s), and retrieve a list of genes which meet the selected criteria. Links to Webminer can be found on the SGD Function and Expression page, the SGD External Links page, and the new Expression Connection resource.

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