SGD Quarterly Newsletter
Posted January 29, 2007
In this issue:
- Changes to Gene Ontology Resources
- RNA Polymerase II Distribution Data Displayed
in Genome Browser
- 2 Micron Plasmid Data Incorporated into SGD
- Transporter Classifications Displayed
- New Microarray Datasets Added to Expression Connection
- Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae
- New or Updated Summary Paragraphs for 35 Genes
- Community News
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About this Newsletter
This is the January 2007 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.
-
SGD has made several changes to Gene Ontology resources:
- Introduction of the Annotation
Type concept to distinguish annotations made from experiments
focusing on specific genes (the Core
annotations), versus those derived from a high-throughput approach (High-throughput
annotations). GO annotations are labeled as Core or High-throughput on
the Locus Summary page, GO Evidence and References page, and the Term
Details page.
- The GO
Term Finder tool has been updated to include
several new functionalities. This tool now allows you to filter the
background set based on feature type (protein, tRNA, etc.), feature
qualifier (Verified, Uncharacterized, Dubious), annotation type (Core,
High-throughput), or the GO evidence code (IMP, IDA, IGI, etc.) of the
annotation.
- The GO
Slim Mapper tool has been updated to allow filtering by annotation
type (Core, High-throughput).
- The Gene
Ontology Consortium (GOC) recently merged the three 'unknown'
terms, biological_process unknown (GOID:0000004), molecular_function
unknown (GOID:0005554) and cellular_component unknown (GOID:0008372)
in the three ontologies to their respective root terms biological
process (GOID:0008150),
molecular function (GOID:0003674)
and cellular component (GOID:0005575)
to improve the ability to do computational reasoning on the
ontology. SGD has updated its annotations to reflect this change. We
have modified the display of the root terms to help make it clear that
annotation to the root nodes indicates lack of knowledge at the time
the annotation was made.
- The distribution of RNA polymerase II (Pol
II) across the
S. cerevisiae genome reported in Steinmetz, et al. 2006
can be viewed in SGD's Genome Browser. To see these data, you
may need to check the "Pol II distribution - Steinmetz, et al (2006)"
track and select the "Update Image" button or the red "Reset" button. The data are available
from SGD's FTP site. Thanks to David Brow and Christopher Warren for
working with SGD on incorporating their data.
- SGD has incorporated the 2 micron plasmid as a genomic
feature and updated the annotations of the four ORFs on the plasmid:
FLP1/R0010W,
REP1/R0020C,
RAF1/R0030W,
and REP2/R0040C.
ORF sequences can be obtained from the individual Locus Summaries or
in files on the FTP
site. The sequence for the entire 2 micron plasmid can be
obtained from GenBank.
The 2 micron plasmid is also now part of SGD's S. cerevisiae BLAST
Search, which has recently been updated to facilitate
selection of a variety of different target sequence datasets.
-
SGD now displays Transporter
Classifications (TC; De
Hertogh et al. 2006) made by the Yeast
Transporter Information (YETI) project, part of the Genolevures
project. The TC numbers assigned to individual proteins are displayed
in the "External Classifications" section of Protein
Information pages, and links to the Transporter
Classification Database (TCDB) are listed in the External Links
sections of both the Locus Summary and the Protein Information
pages. These assignments are also included in the dbxref.tab file on
our FTP
site. Many thanks to Marie-Line Renaut-Seret, Philippe Baret and
Andre Goffeau for their help in incorporating this information.
-
SGD's Expression Connection allows users to search expression patterns
for multiple genes across multiple microarray experiments. Datasets in
Expression Connection are also available for download from SGD's FTP
site. Microarray datasets from two studies have been added to
Expression Connection:
-
"Expression in response to anoxia (0 - 6 generations) and subsequent
reoxygenation (6 - 7.6 generations) in galactose" and "Expression in
response to anoxia (0 - 6 generations) and subsequent reoxygenation (6
- 7.6 generations) in glucose" (Lai
et al. 2006). This study measures the expression of
S. cerevisiae genes during growth under anaerobic conditions
followed by a shift to aerobic conditions, using either galactose or
glucose as carbon sources. Thanks to Kurt Kwast and his group for
contributing their results and for assistance in checking and loading
the data.
-
"Transition from fermentative to glycerol-based respiratory growth" (Roberts
et al 2006). This study measures the expression of
S. cerevisiae genes during a shift from glucose-based fermentative
conditions to glycerol-based respiratory conditions. Thanks to George
Roberts for assistance in checking and loading the data.
-
As new data become available, SGD curators update the systematic
sequence and its annotation. During the last quarter, sequence and/or
annotation changes were made affecting one feature (MET4/YNL103W), and no new
features were added. More detailed information
regarding sequence and annotation changes can be found via the Chromosome
History Search and in the "Locus History" pages of affected
features. Files on the SGD FTP site are updated
weekly.
-
Gene Summary Paragraphs summarize published biological information for
a gene and its product, and are designed to familiarize both yeast and
non-yeast researchers with the general facts and important subtleties
regarding a locus. During the last quarter, gene summary
paragraphs have been added or updated on the Locus Summary pages of the following 35 genes.
-
- The Saccharomyces Genome Resequencing Project (SGRP) has sequenced
14 S. cerevisiae strains and 21 S. paradoxus strains and
the data are now available at the Sanger
Institute. The SGRP
Genome Browser allows users to browse alignments, SNPs and
annotations for the sequenced data. The strains will be available from
the National
Collection of Yeast Cultures (NCYC) as well as from Ed
Louis' Lab. While using these data, the SGRP requests that
researchers adhere to the Data Release Policy posted on their
website. A link to the SGRP website is available from SGD's External
Links page. The SGRP is a collaboration between the Sanger
Institute and Prof. Ed
Louis' group at the Institute of Genetics, University of
Nottingham.
Upcoming Conferences and Courses (*asterisks indicate attendance by SGD)
- 24th Fungal Genetics Conference*
Asilomar Conference Center, Pacific Grove, CA
March 20 - 25, 2007
- XIV Southeastern Regional Yeast Meeting
University of Alabama at Birmingham,
Birmingham, AL
March 31 - April 1, 2007
- Experimental Biology Annual Meeting*
Washington, DC
April 28 - May 2, 2007
- Epigenetics: Regulation of Chromatin Structure in Development and
Disease (D3)*
Beaver Run Resort; Breckenridge, Colorado
April 11 - 16, 2007
- The Biology of Genomes*
Cold Spring Harbor Laboratory, New York
May 8 - 12, 2007
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As always, please contact SGD with any comments or suggestions at:
yeast-curator@yeastgenome.org
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