SGD Quarterly Newsletter, Summer 2007
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
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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