SGD Newsletter
April 2003
In this issue:
New SGD Features
* New version of Expression Connection
* Feature Search (a new Advanced Search)
* New locus page links (DIP, Open Biosystems, SCOP Superfamily, BIND, BLASTP query at NCBI)
* New phenotype data from Steinmetz et al.
* Table of Community Annotations
Community News
Other SGD News
Relevant URLs
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. You have
received it because you are listed as a contact for SGD in our
database. Information on how to unsubscribe is at the bottom of this
newsletter.
Other relevant URLs mentioned in this newsletter can also be found at
the bottom of the page. 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:
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." The lists of genes exhibiting these
phenotypes are found at the URLs below. 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 *
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
(Gene Registry URL provided below).
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.
* URLs mentioned in this newsletter *
Expression Connection:
http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl
Advanced Feature Search:
http://db.yeastgenome.org/cgi-bin/search/featureSearch
DIP:
http://dip.doe-mbi.ucla.edu/dip/Main.cgi
Open Biosystems:
http://www.openbiosystems.com/
SCOP Superfamily:
http://supfam.org/SUPERFAMILY/index.html
Steinmetz et al. reference in SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=36321
Phenotype Results: exhibits growth defect on a non-fermentable
(respiratory) carbon source
http://db.yeastgenome.org/cgi-bin/phenotype/phenotype.pl?phenotype=861
Phenotype Results: Exhibits growth defect on a fermentable carbon
source
http://db.yeastgenome.org/cgi-bin/phenotype/phenotype.pl?phenotype=860
Table of Community Annotations:
http://www.yeastgenome.org/cache/communityTable.html
Submit a Community Annotation:
http://db.yeastgenome.org/cgi-bin/communityAnnotation
CSH Yeast Cell Biology Meeting:
http://meetings.cshl.org/2003/2003yeast.htm
CSH Yeast Genetics Course:
http://meetings.cshl.org/2003/2003c-yeast.htm
YGBM Meeting; Goteborg, Sweden
http://www.yeast2003.se/
International Meeting on Yeast Apoptosis; Smolenice castle, Slovak Republic
http://www.fns.uniba.sk/~kbi/imya/
SGD t-shirt:
http://www.yeastgenome.org/superbud2.html
Gene Registry Form
http://db.yeastgenome.org/cgi-bin/registry/geneRegistry
Webminer:
http://www.yeastgenome.org/cgi-bin/webminer/mkjavascript
