SGD Newsletter
April 2004
In this issue:
What's New at SGD?
1) Sequence updates completed
2) Large-scale genetic interaction data added
3) Large-scale genetic footprinting data added
4) Expanded annotation of the rDNA region
5) New microarray data sets added
6) New Fungal BLAST tool
Community News
Relevant URLs
This is the April 2004 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 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) Sequence updates completed
SGD has recently updated the systematic sequence on several
chromosomes. These sequence changes are based on the re-sequencing of
portions of the S288C strain background. Some of these sequence
changes also result in annotation changes, such as altering the start
or stop codons. In addition, we will have corrected the annotations
for some genes in cases where the sequence was correct, but the
original gene call was not (e.g. new exons/introns, change in the
start methionine, etc.)
During the month of February, sequence and/or annotation updates were
made on the following chromosomes: III, IV, VI, VIII X, XII, XIII,
XIV, and XV. More information about the completed sequence updates can
be found at the Table of Updates to the Systematic Sequence.
2) Large-scale genetic interaction data added
Results from the large-scale genetic interaction study described in
Tong et al. (2004) Science 303:808-813 have been incorporated into
SGD. These genetic interaction data are displayed on individual SGD
locus pages. In addition, you can download all the data from the SGD
ftp site, or from the paper's supplemental web site. Thanks to Amy
Tong and Charlie Boone for assisting SGD in incorporating their
results in order to provide this valuable resource to the yeast
community.
3) Large-scale genetic footprinting data added
Results from a large-scale yeast genetic footprinting study performed
by Dunn et al have been incorporated into SGD. Phenotypic profiling of
individual genes was achieved by assaying the fitness of multiple
independent mutants of each gene during competitive growth under five
different conditions. These results are displayed in the Phenotype
section of individual SGD locus pages. In addition, you can download
all the data from the SGD ftp site. Thanks to Barbara Dunn et al. for
releasing these data and providing an abstract to SGD pre-publication.
4) Expanded annotation of the rDNA region
SGD has expanded its annotation of the S. cerevisiae rDNA locus, RDN1,
which consists of 100-200 tandem copies of a 9.1-kb repeat covering
approximately 1-2 Mb on the right arm of Chromosome XII. In addition
to the three ribosomal RNA coding sequences (for the 18S, 5.8S, and
25S rRNAs), each of the two annotated repeat units (RDN37-1 and
RDN37-2) now contains annotated 5' ETS, 3' ETS, ITS1, ITS2, NTS1, and
NTS2 spacer regions, including respective locus pages. Thanks to David
Tollervey and Christophe Dez for verifying coordinates and providing
feedback for these expanded yeast rDNA annotations.
5) New microarray data sets added
Four data sets have been added to SGD's Expression Connection tool,
which allows you to search gene expression data from multiple
microarray studies. The data sets that have been added are:
* Ploidy regulation of gene expression (Galitski et al. (1999) Science 285:251-4)
* Gene regulation by Swr1, Htz1, and Ino80 (Mizuguchi et al. (2004) Science 303:343-8)
* Expression regulated by the calcineurin/Crz1 pathway (Yoshimoto et
al. J Biol Chem 277:31079-88)
* Expression during the unfolded protein response (Travers et al. Cell 101:249-58)
These data are also available for download on the SGD ftp site. Thanks
to Joe Landry for assisting SGD in loading his data from Mizuguchi et
al.
6) New Fungal BLAST tool
SGD has created a new Fungal BLAST interface that can be used to do
BLASTN (nucleotide vs. nucleotide) or TBLASTN (protein vs. translated
nucleotide database) searches of any sequence of choice against any
combination of fungal sequence datasets, including genome sequences of
fungal model organisms and pathogens, ESTs, and other fungal sequence
sets in GenBank. The tool is accessible from links on the Analysis &
Tools and Homology & Comparisons pages, as well as from the
"Comparison Resources" pull-down menu on all SGD Locus
pages. Additional fungal sequence datasets will be incorporated as new
genomes become available. See SGD's Fungal BLAST help page for more
information.
Community News
==============
1) Ashbya gossypii Genome Database available online
The complete sequence and annotation of the A. gossypii genome has
been made available at the Ashbya Genome Database (AGD) by Peter
Philippsen and colleagues. Results describing how the A. gossypii
genome gives insight into the evolution of the S. cerevisiae genome
can be read in Dietrich et al. (2004) Science 304:304-7. The genome
sequence for A. gossypii is included in the Fungal BLAST tool at SGD.
2) Upcoming conferences and courses
* May 29 - June 3, 2004: Gene Transcription in Yeast: EuroConference
at San Feliu de Guixols, Spain.
* July 10-15, 2004: Yeast Chromosome Structure, Replication and
Segregation at Callaway Gardens, Pine Mountain, GA.
* July 27 - August 1, 2004: 2004 Yeast Genetics & Molecular Biology at
University of Washington, Seattle, WA. Meeting registration ends
June 28, 2004.
* August 18 - August 22, 2004: Third International Meeting on Yeast
Apoptosis (IMYA) at Faculty of Natural Sciences of Salzburg
University, Salzburg, Austria
URLs mentioned in this newsletter
=================================
SGD home page:
http://www.yeastgenome.org/
SGD ftp site:
ftp://genome-ftp.stanford.edu/pub/yeast/
Table of Updates to the Systematic Sequence:
http://www.yeastgenome.org/sequenceupdates.shtml
Annotation changes:
http://www.yeastgenome.org/chromosomeupdates/annotation_changes.html
Tong et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=41829
Tong et al. supplemental web site:
http://www.sciencemag.org/cgi/content/full/303/5659/808/DC1
Download large-scale genetic interaction data from SGD:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/
Dunn et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=41830
Download large-scale genetic footrping data from SGD:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/systematic_results/genetic_footprinting/
RDN1 region:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=RDN1
Expression Connection:
http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl
Galitski et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=11138
Mizuguchi et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=41832
Yoshimoto et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=33818
Travers et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=42375
Download microarray data sets from SGD:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/systematic_results/expression_data/
Fungal BLAST tool:
http://seq.yeastgenome.org/cgi-bin/SGD/nph-blast-fungal.pl
Fungal BLAST help page:
http://www.yeastgenome.org/help/fungal-blast.html
Analysis & Tools page:
http://www.yeastgenome.org/ATContents.shtml
Homology & Comparisons page:
http://www.yeastgenome.org/HCContents.shtml
Ashbya Genome Database:
http://agd.unibas.ch/
Dietrich et al. reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?refNo=42630
Gene Transcription in Yeast: EuroConference
http://www.esf.org/esf_euresco_conference.php?language=0&conference=103&meeting=5&page=1
Yeast Chromosome Structure, Replication and Segregation
http://src.faseb.org/2004_sch.htm
2004 Yeast Genetics & Molecular Biology
http://www.yeast-meet.org/
Third International Meeting on Yeast Apoptosis (IMYA)
http://www.yeast-apoptosis.org/html/
