SGD Newsletter
April 2005
In this issue:
What's New at SGD?
1. Genome Snapshot of S. cerevisiae
2. Full-text Literature Search
3. PSI-BLAST Now Uses UniRef90 Data Set
4. Fungal Alignment Enhancements
5. New Expression Connection Data Sets
6. Batch Download Expanded Data Types
7. Analyze Gene List Enhancements
8. Correction of Systematic Names
9. Addition of interaction data from GRID
Community News
Relevant URLs
This is the April 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. Genome Snapshot of S. cerevisiae
SGD has created a Genome Snapshot page that provides the most
up-to-date count of S. cerevisiae genomic features and a summary of
Gene Ontology (GO) annotations. This page displays a pie-chart showing
the number of Verified, Uncharacterized and Dubious protein coding
genes, an inventory of all the genomic features by chromosome
(breakdown of the number of protein coding ORFs, RNA coding genes,
sequence length, etc.), a summary of GO annotations and the
distribution of GO annotations for S. cerevisiae gene products by
Process, Function and Component Ontologies. The Genome Snapshot page
can be accessed from SGD's Home page under 'SGD Curation News' and
from the Download Data and About SGD contents pages.
2. Full-text Literature Search
A full-text literature search capability has been added to SGD. The
literature search tool is powered by Textpresso, a text-mining tool
developed at Wormbase (Muller H, et al. (2004) PLoS
Biol. 2(11):e309). Currently, the application contains about 14,000
pre-filtered, yeast-related full-text journal articles spanning the
last 10 years. Queries may contain user-defined keywords, either
alone, or in combination with optional category (grouping) terms. The
full-text literature search can be accessed via the Full-text search
link on the home page and is also available as a link on the SGD
Search Options contents page.
3. PSI-BLAST Now Uses UniRef90 Data Set
The PSI-BLAST Results page (previously called the "Sequence Similarity
Query") now displays the results of a precomputed PSI-BLAST analysis
for every S. cerevisiae protein sequence against UniProt's UniRef90
data set. A new download option has been added to this resource so that
sequences of interest can be downloaded in FASTA format. The PSI-BLAST
Results can be accessed from the "Comparison Resources" pulldown menu
on all Locus pages and from the Homology and Comparisons Page. More
information about these data is included in the PSI-BLAST Help page.
4. Fungal Alignment Enhancements
The Fungal Alignment display has been updated with the following
features: Faster retrieval of the default protein alignment; access to
other, non-orthologous sequences; and more alternatives for sequence
download, including the option of downloading multiple sequences
without aligning them. The Fungal Alignment can be accessed from the
"Comparison Resources" pulldown menu on all Locus pages and from the
Homology and Comparisons Page. More information about this program is
included in the Fungal Alignment Help page.
5. New Expression Connection Data Sets
Six new microarray data sets have recently been added to Expression
Connection. We thank Astrid Haugen, Jennifer Collins, Jing Huang,
Haico van Attikum, Olivier Fritsch, and Fred Winston for contributing
their results and assisting us in loading the data. The new data sets
are:
* Expression in the presence of small-molecule inhibitors of
rapamycin (SMIRs) - Huang J, et al. (2004) PNAS
101(47):16594-9
* Expression analysis of snf/swi mutants - Sudarsanam P, et
al. (2000) PNAS 97(7):3364-9
* Expression in response to arsenic (time and dose) and
* Role of transcription factors in adaptation to
arsenic-induced stress - Haugen AC, et al. (2004) Genome Biol
5(12):R95
* Gene regulation by Ino80 and Arp8 and
* Gene regulation by Ino80 and Arp8 in response to MMS - van
Attikum H, et al. (2004) Cell 119(6):777-88
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. The data sets used in the Expression Connection tool are
also available for download on the SGD ftp site.
6. Batch Download Expanded Data Types
The functionality of the Batch Download Tool has been updated to
facilitate the retrieval of two new types of data:
1) Phenotypes in SGD's phenotypes.tab format
2) Genetic and Physical Interactions in a tab-delimited format
As with the other Batch Download options, these data can be retrieved
using as input a list of gene names, feature names or SGDIDs. These
newly available data types can be retrieved simultaneously with DNA
sequences, protein sequences, and chromosomal coordinate information
for the same input list. In addition, this tool now also allows
retrieval of all the features within a chromosome without having to
enter the beginning and end coordinates of the chromosome.
7. Analyze Gene List Enhancements
The Analyze Gene List module, available on the results pages of the
Advanced Search tool, Expression Connection, Webminer and All
Interactions, has been updated. It now links to the Batch Download
tool and provides brief descriptions of the available options.
8. Correction of Systematic names
In partnership with Munich Information Center for Protein Sequences
(MIPS), SGD has re-examined the systematic names of 22 small ORFs
which were incorrect at one or both of our databases. In most cases,
either MIPS or SGD changed to the systematic name used by the other
database. In some cases, we chose to use a different name altogether,
and the systematic name was changed at both databases. SGD has
corrected the systematic names of 12 small ORFs and MIPS has corrected
the systematic names of 13 small ORFs (3 systematic names were
corrected at both databases). All SGDIDs and coordinates remain
unchanged. All systematic names used at either database will remain
associated with the appropriate ORF, either as systematic names or as
aliases. A summary of these corrections has been posted at SGD. Please
note that researchers should not publish systematic names for newly
discovered protein coding ORFs without prior consultation with SGD;
please see the Systematic Names Help page for more information on how
newly discovered ORFs are assigned systematic names.
9. Addition of interaction data from GRID
We have added over 15,000 genetic and physical interactions provided
by the GRID interaction database to SGD. The current GRID data set
(downloaded on April 17 from the GRID download page) contains
interactions curated from individual papers, high throughput studies,
and the BIND and MIPS databases. These data can be viewed on the web
on SGD Locus Pages, with links to pages that contain more detailed
information about the interaction, such as the source of the
information, the type of interaction, etc. In addition, the data are
available for download from the SGD and GRID ftp sites. Thanks to
Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, and Mike Tyers for
providing this resource to the community and for helping us load these
data into SGD.
Community News
==============
* May 11 - May 15, 2005 The Biology of Genomes, Cold Spring Harbor
Laboratory, Cold Spring Harbor, NY
* May 12 - May 14, 2005 Seventh International Yeast Lipid Conference,
University of Wales Swansea, UK
* May 21 - May 28, 2005 FEBS Advanced Lecture Course on Human Fungal
Pathogens: Molecular Mechanisms of Host-Pathogen Interactions and
Virulence, La Colle sur Loup, France
* June 10 - June 12, 2005 Conference on Numbers to the models:
Generating the data for Systems Biology, Goteborg, Sweden
* 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
* 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
Relevant URLs
=============
For What's New items
---------------------
SGD Homepage
http://www.yeastgenome.org/
Genome Snapshot of S. cerevisiae
http://www.yeastgenome.org/cache/genomeSnapshot.html
Full-text Search
http://www.yeastgenome.org/textpresso/
Search Options Page
http://www.yeastgenome.org/SearchContents.shtml
Full-text Literature Search Help Page
http://www.yeastgenome.org/help/textpresso_help.html
Muller H, et al. reference at SGD
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000081385
Homology and Comparisons Page
http://www.yeastgenome.org/HCContents.shtml
PSI-BLAST Results Help Page
http://www.yeastgenome.org/help/SeqSimQuery.html
Fungal Alignment Help Page
http://db.yeastgenome.org/cgi-bin/FUNGI/showAlign
Expression Connection Tool
http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl
Huang J, et al. reference at SGD
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079695
Sudarsanam P, et al. reference at SGD
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000072288
Haugen AC, et al. reference at SGD
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080191
van Attikum H, et al. reference at SGD
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000080061
FTP Site For Expression Connection Data Sets
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/systematic_results/expression_data/expression_connection_data/
Batch Download Tool
http://db.yeastgenome.org/cgi-bin/batchDownload
Analyze Gene List Example
http://db.yeastgenome.org/cgi-bin/phenotype/phenotype.pl?locus=PHO85&type=allinteractions#analyze
Munich Information Center for Protein Sequences (MIPS)
http://mips.gsf.de/genre/proj/yeast/
Summary of Changes to Systematic Names
http://www.yeastgenome.org/chromosomeupdates/SysName-change-summary.html
SGD Help: Systematic Names
http://www.yeastgenome.org/help/SystematicNamesHelp.html
GRID
http://biodata.mshri.on.ca/yeast_grid/servlet/SearchPage
BIND
http://bind.ca/
For Community News items:
-------------------------
Cold Spring Harbor Biology of Genomes
http://meetings.cshl.edu/meetings/genome05.shtml
Seventh International Yeast Lipid Conference
http://www.yeastlipidconference.swan.ac.uk/
FEBS Lecture Course on Human Fungal Pathogens
http://www.pasteur.fr/infosci/conf/hfp2005/Introduction.html
Numbers to the models: Generating the data for Systems Biology
http://www.gmm.gu.se/QUASI/workshop2005.htm
International Conference on Yeast Genetics and
Molecular Biology in Bratislava
http://yeast2005.org
Cold Spring Harbor Yeast Cell Biology
http://meetings.cshl.edu/meetings/yeast05.shtml
Cold Spring Harbor Genome Informatics
http://meetings.cshl.edu/meetings/info05.shtml
Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome
Evolution, Approaches with Yeasts and Fungi
http://www.esf.org/esf_genericpage.php?section=10&language=0&genericpage=2214&shortcut=1
