SGD Quarterly Newsletter, Winter 2010

About this newsletter:

This is the January 2010 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 files available from SGD

The following changes will be made to files available for download from SGD in February 2010:

• All files available in http://downloads.yeastgenome.org/gene_registry/ will be obsoleted. This means that they will no longer be available to download.
• The annotation_change.tab file will also be obsoleted. This means this file will no longer be available to download. For information regarding ORF qualifiers (Verified, Uncharacterized, Dubious), please use the already available SGD_features.tab file. Information regarding deleted or merged chromosomal features can be found in the new deleted_merged_features.tab file (described below).
• A new file called deleted_merged_features.tab will be available from http://downloads.yeastgenome.org/chromosomal_feature/. This file will list chromosomal features that have been deleted or merged. The format of the file is identical to the annotation_change.tab file.

New genetic interaction data file available for download from SGD

A large set of genetic interaction data from Costanzo et al., The Genetic Landscape of a Cell, Science 327: 425-431 (2010) is available for download from SGD's Download Data Files page and will be available via the web interface in the future. This study presents 74,984 genetic interactions, comprising a functional map of the cell. Thanks to the authors for providing their data to SGD. Costanzo et al. 2010: http://www.sciencemag.org/cgi/content/abstract/327/5964/425 Download the data set from SGD: http://downloads.yeastgenome.org/systematic_results/genetic_interactions/Costanzo_2010_pmid_20093466

Gene Ontology (GO) Reference Genome Annotations

What is it?

The goal of the Gene Ontology Consortium (GOC) Reference Genome Annotation Project is to provide comprehensive sets of annotations for all gene products in 12 "reference genomes", which can be used to facilitate the study of human disease, and also to seed automatic inferencing for the annotation of newly-sequenced genomes. Saccharomyces cerevisiae is one of the 12 reference genomes and SGD is actively involved in this annotation effort by providing annotations for yeast gene products.

GO Reference Genome Project: http://www.geneontology.org/GO.refgenome

Where can these annotations be viewed?

Annotations included as part of the Reference Genome Annotation Project can be viewed using the GOC's 'AmiGO' browser and search tool. The Homolog Sets page lists the genes in the various homolog families from the various organisms that have been annotated thus far, as well as the type of experimental evidence that supports the annotations for each gene. Various navigation options are available for viewing the annotations. Homolog Set Summary in AmiGO: http://amigo.geneontology.org/cgi-bin/amigo/amigo?mode=homolset_summary

Sequence and Annotation Updates

SGD curators periodically update the systematic sequence and its annotation. Information regarding 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. Between 2010-01-04 and 2010-01-05, two new ncRNAs (ICR1 and PWR1) were annotated on Chromosome IX, the annotation of ORF DIA2/YOR080W was changed, and the sequence of Chromosome XIV was changed, affecting the annotation of ORF SAL1/YNL083W.

Summary of Chromosome Sequence and Annotation Updates: http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl

Locus History search: http://www.yeastgenome.org/cgi-bin/locusHistory.pl

New Gene 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 new summary paragraphs have been added to their respective Locus Summary pages for 23 features.

Genes with new summary paragraphs are reported weekly on SGD's "What's New" page: http://www.yeastgenome.org/whats_new.shtml

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

• 17th Annual Southeastern Regional Yeast Meeting

Little Rock, Arkansas

March 12-14, 2010

• Systems Biology: Global Regulation of Gene Expression

Cold Spring Harbor, New York

March 23-27, 2010

• The Biology of Genomes

Cold Spring Harbor, New York

May 11-15, 2010

• Genetics 2010: Model Organisms to Human Biology

Boston, Massachusetts

June 12-15, 2010

• EMBO Yeast Transcription Conference 2010

San Feliu de Guixols, Spain

June 19-24, 2010

• Genetics of Industrial Microogransims

Melbourne, Austraila

June 28 - July 1, 2010

• ISMB2010

18th Annual International Conference on Intelligent Systems for Molecular Biology

Boston, Massachusetts

July 11-13, 2010

• MGED

13th Internation Meeting of the Microarray and Gene Expression Data Society

Boston, Massachusetts

July 13-15, 2010

• Yeast Genetics and Molecular Biology Meeting

Vancouver, Canada

July 27 - August 1, 2010

• Society for Industrial Microbiology 60th Annual Meeting

San Francisco, California

August 1-5, 2010

• Systems Biology: Networks

Hinxton, UK

August 11-15, 2010

• Genome Informatics

Hinxton, UK

September 15-19, 2010

• XV International Conference on Yeast Genetics and Molecular Biology

Olsztyn, Poland

July 11-16, 2011

asterisks indicate attendance by SGD.*

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