SGD Newsletter
July 2005
In this issue:
What's New at SGD?
1. Navigation tabs
2. Primer sequences added in GBrowse
3. A new microarray data set
4. New gene summary paragraphs for 36 genes
involved in N-linked glycosylation
5. Large scale phenotype data added
6. Deletion strain barcode arrays now available
7. Bratislava abstracts available online
Community News
Relevant URLs
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. 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.
If you think friends or colleagues would be interested in receiving
this newsletter, they can subscribe by filling out an SGD colleague
form, found using this url:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch
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
What's New at SGD?
==================
1. 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.
2. 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.
3. 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.
4. 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.
5. 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).
6. 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.
7. 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
==============
1) 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.
2) Addgene: Repository and distributor of plasmid constructs described
in published literature.
3) Upcoming conferences
* 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
Relevant URLs
=============
For What's New items
---------------------
SGD Homepage:
http://www.yeastgenome.org/
Gbrowse:
http://db.yeastgenome.org/cgi-bin/gbrowse/yeast
Expression Connection:
http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl
Mnaimneh, S., et al. (2004), reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000076598
ALG7 Locus Page:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ALG7
OST3 Locus Page:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=OST3
GFA1 Locus Page:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GFA1
Lesage, G., et al. (2005) reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080816
Deutschbauer, A.M., et al. (2005) reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080907
Xie, M.X., et al. (2005) reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000081669
Barcode home page:
http://barcode.princeton.edu/
SLAM home page:
http://slam.bs.jhmi.edu/
XXIIth International Conference on Yeast Genetics and Molecular Biology:
http://www.yeast2005.org/
Bratislava Abstract search form:
http://www.yeastgenome.org/community/meetings/yeast05/
For Community News items:
-------------------------
CryptoBase:
http://cryptogenome.ucsf.edu/
Addgene:
http://www.addgene.org/pgvec1
Cold Spring Harbor Yeast Cell Biology:
http://meetings.cshl.edu/meetings/yeast05.shtml
Conference on AAA Proteins:
http://mikrobiologie.uni-graz.at/public/AAA-conference/
Cold Spring Harbor Genome Informatics:
http://meetings.cshl.edu/meetings/info05.shtml
Comparative Genomics of Eukaryotic Microorganisms:
http://www.esf.org/esf_genericpage.php?section=10&language=0&genericpage=2214&shortcut=1
Meeting on Yeast and Apoptosis:
http://www.yeast-apoptosis.org/miami/
Genetic Analysis: Model Organisms to Human Biology:
http://www.gsa-modelorganisms.org/
23rd International Conference on Yeast Genetics and Molecular Biology:
http://www.yeast2007.org/
