SGD Quarterly Newsletter, Spring 2006
About this newsletter:
This is the May 2006 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.
Contents
- 1 Collaboation with BioGRID Makes 65,000+ Interactions Available at SGD
- 2 New Topics for Expanded Literature Curation
- 3 Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae
- 4 Batch Download Tool Improved
- 5 Links to YOGY Tool Added
- 6 BioPIXIE Data and Links Incorporated
- 7 SAGE Data Remapped to Updated Sequence
- 8 New Summary Paragraphs for 59 Genes
- 9 New Datasets Added
- 10 Community News
- 11 Upcoming Conferences and Courses
Collaboation with BioGRID Makes 65,000+ Interactions Available at SGD
SGD has joined forces with BioGRID to provide a common dataset of budding yeast interactions. More than 65,000 genetic and physical interactions are now available from SGD. This dataset is described by Reguly et al. (2006), Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces cerevisiae, Journal of Biology, in press. SGD, BioGRID and the SGD Colony at Princeton are working together to maintain and update this complete dataset of yeast genetic and physical interactions. We thank Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark for their help in providing and loading the data.
New Topics for Expanded Literature Curation
SGD has expanded literature curation procedures to better annotate papers that describe the biology of S. cerevisiae without investigating the function(s) of specific gene(s). In order to capture the range of topics addressed in these papers, the following new Topics have been added to the Literature Guide: Cell Growth and Metabolism, Infection and Antifungals, Industrial Applications, Evolution, and Nucleic Acid Interaction. Papers grouped according to new and existing Literature Topics are accessible from the SGD Curated Paper page for any reference in SGD. For example, clicking on the green ball of the curated paper page for Henry et al. (2004) retrieves a list of all references curated for the topic "Infection and Antifungals".
Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae
SGD curators have updated the systematic sequence and its annotation. Sequence and/or annotation changes were made affecting 9 features, and 11 new features have been added. Altered or new features are listed in the What's New in SGD for 2006. Details regarding these changes can be found in the Table of Sequence Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. The following table lists the sequence changes made during the last quarter.
List of Sequence/Annotation Changes
| Chromosome | Sequence/Annotation Changes | New Features Added |
|---|---|---|
| I | None | ARS110 |
| II | None | ARS209 |
| III | None | None |
| IV | ARS1/ARS416, YDR015C, SIP1/YDR422C, PEX19/YDL065C, MGT1/YDL200C, RRI1/YDL216C | HED1/YDR014W-A, ARS404, ARS422 |
| V | None | None |
| VI | None | ARS600 |
| VII | None | ARS706 |
| VIII | ARS2/ARS808 | ARS805 |
| IX | None | None |
| X | None | None |
| XI | None | SNR87/snR87 |
| XII | YLR312C-B, SPH1/YLR313C | ARS1208 |
| XIII | None | None |
| XIV | None | None |
| XV | None | ARS1516 |
| XVI | None | None |
| Mito | None | None |
Batch Download Tool Improved
The Batch Download tool has been updated to allow simultaneous retrieval of data for features from several chromosomes or chromosomal regions. A file specifying chromosomal regions or simply chromosome numbers may now be uploaded on this interface to retrieve different types of data for the features included in the chromosomal regions or chromosomes. The Batch Download tool can be accessed through links on the Analysis & Tools and Download Data contents pages.
Links to YOGY Tool Added
Links to eukarYotic OrtholoGY (YOGY), a tool to view orthologous proteins from eukaryotic organisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae), have been added to the Model Organism BLASTP Best Hits page and the Comparison Resources pull-down menu on Locus Summary Pages. This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL, and manually curated orthologs between S. cerevisiae and S. pombe. YOGY was developed by the Fission Yeast Functional Genomics Team at the Wellcome Trust Sanger Institute, Cambridge, UK.
BioPIXIE Data and Links Incorporated
SGD has added the data from Myers et al. (2005), a study that describes a novel system for data integration and visualization, to the SGD FTP site. In addition, links are provided to the accompanying BioPIXIE tool, which allows you to search and visualize interaction networks involving your gene(s) of interest; these links can be found on all Locus Summary Pages within the Interactions pull-down menu on the right side of the page. Thanks to Chad Myers in Olga Troyanskaya's lab at the Lewis-Sigler Institute of Integrative Genomics, Princeton, NJ for providing this information to SGD.
SAGE Data Remapped to Updated Sequence
The SAGE data published by Velculescu et al. (1997) have been remapped to the recently updated S. cerevisiae systematic sequence. SAGE tags can be displayed in the ORF Map and by selecting the "SAGE tags" track option in GBrowse (Genome Browser). The scerevisiae_sage.gff file and corresponding README are available from our FTP site.
New Summary Paragraphs for 59 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, new gene summary paragraphs for the following 59 genes have been added to their respective Locus Summary Pages.
List of Gene Summary Paragraphs Added During the Last Quarter
New Datasets Added
- A set of files detailing the sequence and location of every palindrome in the S. cerevisiae genome has been added to SGD's FTP site. The data were generated in a study published by Lisnic et al. (2005). Many thanks to Berislav Lisnic for contributing the results and for assistance with the files.
- A new microarray dataset, "Expression in response to peroxisome induction and repression" (Smith et al. 2002), has been added to Expression Connection. This study compares the expression of each S. cerevisiae gene during metabolic shifts that either induce or repress peroxisome assembly and proliferation to identify genes involved in peroxisome biogenesis or function. We thank John Aitchison and Jennifer Smith for contributing their results and assisting us in loading the data. 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 menu located on the right side of the Locus Summary Page or by clicking on the Expression Summary histogram. In addition, in order to provide a better representation of expression ratios over an increasing number of experiments the Expression Summary histogram has recently been modified for finer binning. Datasets in Expression Connection are also available for download from the SGD FTP site.
Community News
Programming position available at SGD
- We are looking for a motivated, experienced senior bioinformatician to help maintain and enhance the web pages and tools available at SGD. A detailed description of the position as well as instructions for applying can be found in the job posting on Stanford's job website. Applications must be submitted via Stanford Jobs.
Upcoming Conferences and Courses
Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses
- ESF-EMBO Symposium on Gene Transcription in Yeast*
- Sant Feliu de Guixols, Spain
- June 24 - June 29, 2006
- Yeast Chromosome Structure, Replication and Segregation (FASEB)*
- Indian Wells, CA
- June 24 - June 29, 2006
- 2006 Yeast Genetics and Molecular Biology Meeting*
- Princeton University, Princeton, NJ
- July 25 - July 30, 2006
- 24th Small Meeting on Yeast Transport and Energetics
- Prague, Czech Republic
- August 31 - September 3, 2006
- 5th International Meeting on Yeast Apoptosis
- Kutna Hora, Czech Republic
- September 3 - September 7, 2006
- XXIIIrd International Conference on Yeast Genetics and Molecular Biology*
- Melbourne, Australia
- July 1 - July 6, 2007
asterisks indicate attendance by SGD.*
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