SGD Quarterly Newsletter, Winter 2007

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 can also subscribe to SGD's RSS feed to receive updates on SGD news - http://www.yeastgenome.org/feed

Changes to Gene Ontology Resources

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.

RNA Polymerase II Distribution Data Displayed in Genome Browser

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.

2 Micron Plasmid Data Incorporated into SGD

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.

Transporter Classifications Displayed

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 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.

New Microarray Datasets Added to Expression Connection

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.

Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae

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.

New or Updated Summary Paragraphs for 35 genes

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.

Summary Paragraphs Added or Updated During the Last Quarter

CCH1/YGR217W	COX11/YPL132W	FKH1/YIL131C	FKH2/YNL068C	GCD1/YOR260W
GCD2/YGR083C	GCD6/YDR211W	GCD7/YLR291C	GCN3/YKR026C	GLK1/YCL040W
GSH1/YJL101C	HCM1/YCR065W	HML	HMR	HSF1/YGL073W
HXK1/YFR053C	HXK2/YGL253W	IZH1/YDR492W	IZH2/YOL002C	IZH3/YLR023C
IZH4/YOL101C	MAT	MSN2/YMR037C	MSN4/YKL062W	PBS2/YJL128C
PET100/YDR079W	PMC1/YGL006W	PMR1/YGL167C	RAD55/YDR076W	RAD57/YDR004W
STV1/YMR054W	TAZ1/YPR140W	VCX1/YDL128W	VPH1/YOR270C	YDJ1/YNL064C

Comunity News

• 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 Meetings

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

• 24th Fungal Genetics Conference

Asiloar 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

asterisks indicate attendance by SGD.*

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