SGD Quarterly Newsletter, Spring 2003
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: yeast-curator@genome.stanford.edu
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:
- Search multiple datasets for expression results using one or more gene names.
- Find datasets where the expression of one or more genes changes by an amount you define.
- 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: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses
- 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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