SGD Quarterly Newsletter, Fall 2005
About this newsletter:
This is the October 2005 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.
Other relevant URLs mentioned in this newsletter are also at the bottom of the page. As always, please contact SGD with any comments or suggestions at: firstname.lastname@example.org
- 1 Transcription factor data added
- 2 Protein domains predicted using InterProScan
- 3 SGD links to the Candida Genome Database
- 4 Enhancement to SGD Quick Search
- 5 New Expression Connection dataset added - glycosylation
- 6 Complete set of Descriptions for protein coding genes
- 7 New gene summary paragraphs
- 8 Community News
Transcription factor data added
A new "Regulatory Role" section has been added to the Locus Summaries for many known transcriptional regulators. This section displays DNA-binding motifs for these transcription factors and provides links to predicted regulatory modules in which they may be involved [as predicted by Segal et al. 2003]. DNA-binding sites for 102 transcriptional regulators [as mapped by Harbison et al. 2004] have also been added as a "Regulatory regions and binding sites" track to the GBrowse map viewer, and an expanded thumbnail of this viewer now appears in the "Sequence Information" section of the Locus Summary. The GFF file for these binding sites is available from the ftp site. Please see the SUM1 Locus Summary for an example of the new transcription factor data.
Protein domains predicted using InterProScan
SGD displays Protein Domains and Motifs predicted by comparing S. cerevisiae protein sequences against sequences in the InterPro Database using the InterProScan program (Quevillon et al. 2005). The InterPro Database integrates motif and domain information from the Prosite, PRINTS, SMART, ProDom, TIGERFAMs and PIR Superfamily databases. Protein Domains/Motifs can be accessed from the "Locus Summary" and "Homology and Comparisons" pages. InterProScan results for all S. cerevisiae proteins are also available for download from SGD's ftp site.
The "Comparison Resources" pull-down menu (located on the right hand side of Locus Summary Pages) now includes links between S. cerevisiae genes and Candida albicans homologs identified at the Candida Genome Database (CGD). Thanks to Gavin Sherlock and Martha Arnaud for providing homology determinations using software developed by Inparanoid.
Enhancement to SGD Quick Search
PubMed IDs (e.g., 15608219) and Gene Ontology (GO) IDs (e.g., GO:0007117) can now be entered into the Quick Search box located at the top of most SGD pages. An exact match to a PubMed ID will display information about how the paper is curated for the Literature Guide, while an exact match to a GO ID will display information about the GO term and what genes have been annotated to that GO term at SGD. Note that the PubMed ID search only works on publications that have been added to SGD. If you notice that SGD is missing a relevant publication, please contact SGD curators and we will happily add it to the database.
New Expression Connection dataset added - glycosylation
A new microarray dataset, "Effects of glycosylation defects on gene expression" (Cullen et al. 2004), has been added to Expression Connection. This study compares the expression profiles of all genes in cells undergoing a conditional protein glycosylation defect induced in a pmi40-101 mutant by growing cells in medium lacking mannose and comparing to cells grown in media supplemented with mannose. A second experiment identifies those genes whose expression in the glycosylation mutant is dependent on the transcription factor Ste12p.
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 or by clicking on the Expression Summary histogram. Datasets in Expression Connection are also available for download from SGD's ftp site.
Complete set of Descriptions for protein coding genes
An effort to update the Description line for all protein coding genes was initiated in 2003 and completed in October 2005. The Description has a 240-character limit and is exported to files available on the SGD ftp site as well as to GenBank RefSeq records. These clear, concise, and up-to-date Description lines are also displayed in other NCBI records, including BLAST results.
New gene summary paragraphs
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 71 genes have been added to their respective Locus Summaries:
Upcoming conferences (*asterisks indicate attendance by SGD)
- October 28 - November 1, 2005
- Genome Informatics
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- November 12 - November 17, 2005
- Comparative Genomics of Eukaryotic Microorganisms:
- Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi
- Sant Feliu de Guixols, Spain
- November 13 - November 17, 2005
- 4th International Meeting on Yeast Apoptosis
- Wyndham Miami Beach Resort, Miami, FL
- January 5 - January 7, 2006
- Genetic Analysis: Model Organisms to Human Biology
- San Diego, California
- July 25 - July 30, 2006
- 2006 Yeast Genetics and Molecular Biology Meeting
- Princeton University, Princeton, NJ
- July 1 - July 6, 2007
- XXIIIrd International Conference on Yeast Genetics and Molecular Biology
- Melbourne, Australia
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