SGD Quarterly Newsletter, Summer 2007

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About this newsletter:

This is the July 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

Contents

Transcription Data in Genome Browser

Transcription start sites reported in Zhang Z and Dietrich FS (2005) Nucleic Acid Res 33:2838 and cDNA clones reported in Miura F et al. (2006) Proc Natl Acad Sci USA 103:17846 can be viewed in the Genome Browser. To view these data, select the "cDNA transcripts" and "Transcription start sites" tracks and press the "Update Image" button. If you do not see those tracks, select the red "Reset" button. The data are available from SGD's FTP site. Thanks to Takashi Ito, Fumihito Miura, Shinichi Morishita, and Fred Dietrich for working with SGD on incorporating these data.

How many Uncharacterized yeast genes?

Huges & Pena-Castillo's paper Why are there still over 1000 uncharacterized yeast genes? is available as a PDF from SGD's FTP site. We thank Genetics for generously providing the freely distributable PDF of this paper. In addition, the list of Uncharacterized ORFs analyzed in this recent publication is available from the same location of the FTP site. SGD staff have reviewed the status of the 126 named genes mentioned in the paper and have upgraded over half of them to Verified status based on recent publications. A current list of Uncharacterized ORFs can be retrieved via SGD's Genome Snapshot or Advanced Search. SGD classifies ORFs as Verified, Uncharacterized, and Dubious according to the degree of certainty that each ORF encodes a functional protein. SGD considers these classifications a working hypothesis, and the designations change based on published experimental results.

Links to Protein, Strain and Expression Websites Added

  • Links to SCEPTRANS, a resource to view and analyze periodic transcription profiles from multiple publications, has been added to SGD. SCEPTRANS can be accessed by selecting the 'Cell cycle and metabolic oscillation' option in the Functional Analysis pull-down menu on Locus Summary Pages for all systematically named ORFs. See Kudlicki A et al. (2007) Bioinformatics for more information. Thanks to Andrzej Kudlicki for generating the summary pages for each ORF.
  • Links to structural annotations for predicted domains at the Yeast Resource Center Public Data Repository have been added for 4640 proteins. These links are available via the "Protein Info" tab at the top of the Locus Summary page and through the "Protein Info & Structure" pull-down menu located on the right side of the Locus Summary page. See Malmstrom et al. PLoS Biol. 2007 for more information. Thanks to Michael Riffle and Trisha Davis for setting up the links.
  • Links to the Yeast Genetics Resource Center, a strain and plasmid resource in Japan, have been added for all ORFs. These links are available via the "Phenotypes" tab at the top of the Locus Summary page for each ORF. Thanks to Chikashi Shimoda and Yukiko Yamazaki for setting up the links.

Improvements to SGD software

Over the past six months, SGD staff have worked to improve the software that generates SGD web pages. As a consequence, many pages, including the Locus Summary and Literature Guide pages, have the same information and layout, but have been restyled for a more uniform, updated look. These changes will facilitate future expansion at SGD. Please do not hesitate to contact us with any bug reports or comments.

New Summary Paragraphs

Summary Paragraphs summarize published biological information for a gene/feature, 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 (May - July 2007), new summary paragraphs for the following 159 features have been added to their respective Locus Summary pages.


List of Summary Paragraphs Added During the Last Quarter
AGC1/YPR021C BCY1/YIL033C CDC13/YDL220C CDC34/YDR054C CMD1/YBR109C
COB/Q0105 COR1/YBL045C CYR1/YJL005W CYT1/YOR065W DNL4/YOR005C
EST1/YLR233C EST2/YLR318W EST3/YIL009C-A FKS1/YLR342W FKS3/YMR306W
FUS3/YBL016W GAS1/YMR307W GAS2/YLR343W GAS3/YMR215W GAS4/YOL132W
GAS5/YOL030W GPA1/YHR005C GSC2/YGR032W HHO1/YPL127C HSP26/YBR072W
HSP42/YDR171W HTA1/YDR225W HTA2/YBL003C KSS1/YGR040W LIF1/YGL090W
MLH2/YLR035C MLH3/YPL164C PAC1/YOR269W PDC1/YLR044C PDC5/YLR134W
PDC6/YGR087C PEX1/YKL197C PEX2/YJL210W PEX3/YDR329C PEX5/YDR244W
PEX6/YNL329C PEX7/YDR142C PEX10/YDR265W PEX12/YMR026C PEX13/YLR191W
PEX14/YGL153W PEX17/YNL214W PEX18/YHR160C PEX19/YDL065C PEX21/YGR239C
PMS1/YNL082W POL30/YBR088C PRC1/YMR297W QCR2/YPR191W QCR6/YFR033C
QCR7/YDR529C QCR8/YJL166W QCR9/YGR183C QCR10/YHR001W-A RAD26/YJR035W
RIP1/YEL024W RPS19A/YOL121C RPS19B/YNL302C SCS2/YER120W SCS22/YBL091C-A
SDP1/YIL113W SPO11/YHL022C SST2/YLR452C SUC1/SUC1 SUC2/YIL162W
SUC3/SUC3 SUC4/SUC4 SUC5/SUC5 SUC7/SUC7 TLC1/TLC1
TPK1/YJL164C TPK2/YPL203W TPK3/YKL166C UGA1/YGR019W UGA2/YBR006W
YAP1/YML007W YKU70/YMR284W YKU80/YMR106C 76 snoRNA genes

Annotation Changes Made to the Systematic Sequence of S. cerevisiae

As new data become available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found via the Summary of Chromosome Sequence and Annotation Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. During the last quarter (May - July 2007), annotation changes were made affecting 10 RNA genes and new introns were annotated within 9 protein-coding features. 1 new feature was added.

Chromosome Annotation Changes New Features
I snR18, HRA1 None
II HPC2/YBR215W None
III None None
IV IWR1/YDL115C None
V GIM4/YEL003W None
VI None None
VII snR46 None
VIII PTC7/YHR076W None
IX None None
X snR3 None
XI None None
XII snR30, snR34 None
XIII snR78, CGI121/YML036W, RPL20A/YMR242C None
XIV HRB1/YNL004W None
XV snR35, snR36, RPL20B/YOR312C None
XVI snR70, YPR153W YPR010C-A

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

  • Yeast Cell Biology*
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
August 15 - 19, 2007
Abstract Deadline: May 23, 2007
  • ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution
Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain
October 20 - 25, 2007
Abstract Deadline: August 1, 2007
  • Genome Informatics*
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
November 1 - 5, 2007
Abstract Deadline: August 1, 2007
  • Genetic Analysis: Model Organisms to Human Biology Meeting
Town and Country Resort & Conference Center, San Diego, CA
January 5 - 9, 2008
Abstract Deadline: November 14, 2007
  • Cellular & Molecular Fungal Biology
Holderness School, Plymouth, NH
June 29 - July 4, 2008
Application Deadline: June 8, 2008
  • Yeast Genetics and Molecular Biology Meeting*
University of Toronto, Toronto, Ontario, Canada
July 22-27, 2008
Abstract Deadline: TBA
For more information contact: mahoney@genetics-gsa.org
  • Plant & Fungal Cytoskeleton
Il Ciocco, Lucca (Barga), Italy
August 3 - 8, 2008
Application Deadline: July 13, 2008


asterisks indicate attendance by SGD.*

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