SGD Quarterly Newsletter, Fall 2007
About this newsletter:
This is the November 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 have received it because you are listed as a contact for SGD in our database.
Contents
- 1 Gene Focus: S. cerevisiae PEXs and Human PBDs
- 2 Computational predictions added to SGD
- 3 New links added: GI numbers, Ortholog resources, an organelle database, and a new microarray search tool
- 4 Antibodies list started in Wiki
- 5 SGD respect your privacy
- 6 81 New Summary Paragraphs
- 7 3 Sequence/annotation changes made to the systematic sequence of S. cerevisiae
- 8 Upcoming Conferences and Courses
Gene Focus: S. cerevisiae PEXs and Human PBDs
The GO consortium is currently working on a project to collectively annotate all model organism genes with homologs involved in human diseases. As part of this project, SGD curators have recently revised and updated our annotations on yeast PEX genes. From yeast to man, the biogenesis of peroxisomes requires a group of conserved "peroxin" protein factors encoded by the PEX genes. In humans, failure to properly develop or maintain peroxisomes leads to peroxisome biogenesis disorders (PBDs), a group of rare, genetically heterogeneous diseases characterized by severe mental retardation, neuronal, hepatic and renal abnormalities, and death in early infancy. In many cases, the genetic defects underlying PBDs have been identified. These mutations fall into at least 14 different complementation groups, and all affect the import of one or more classes of peroxisomal proteins. This cellular phenotype is shared by yeast pex mutants, and the study of pex mutants and peroxisome biogenesis in S. cerevisiae has enhanced our understanding of how the human orthologs function. For complete references and many more details, please see the individual locus pages for these genes (listed in the following table).
| Gene Function | S. cerevisiae Gene (links to SGD) | Human Gene (links to OMIM) |
Associated Human Disease | PBD group |
|---|---|---|---|---|
| Peroxisomal membrane protein import | PEX3 | PEX3 | Zellweger syndrome spectrum | 12 |
| None | PEX16 | Zellweger syndrome spectrum | 9 | |
| PEX 19 | PXF | Zellweger syndrome spectrum | 14 | |
| Receptor for Peroxisomal Targeting Sequence 1 (PTS1) | PEX 5 | PEX5 (aka PTS1R or PXR1) |
Zellweger syndrome spectrum | 2 |
| Receptor for Peroxisomal Targeting Sequence 2 (PTS2) | PEX 7 | PEX7 | rhizomelic chondrodysplasia punctata, type 1 | 11 |
| PTS2 receptor accessory factor | PEX18 | None; Pex5pL may be functional equivalent | --- | --- |
| PEX21 | None; Pex5pL may be functional equivalent | --- | --- | |
| Docking complex component | PEX13 | PEX13 | Zellweger syndrome spectrum | 13 |
| PEX14 | PEX14 | Zellweger syndrome spectrum | ||
| PEX17 | None | --- | --- | |
| Translocation complex component | PEX2 | PXMP3 | Zellweger syndrome spectrum | 5, 10 |
| PEX10 | PEX10 | Zellweger syndrome spectrum | 7 | |
| PEX12 | PEX12 | Zellweger syndrome spectrum | 3 | |
| Association between the docking complex and the translocation complex | PEX8 | None | --- | --- |
| Receptor recycling | PEX1 | PEX1 | Zellweger syndrome spectrum | 1 |
| PEX4 | None | --- | --- | |
| PEX6 | PEX6 | Zellweger syndrome spectrum | 4, 6 | |
| PEX15 | None | --- | --- | |
| PEX22 | None | --- | --- | |
| None | PEX26 | Zellweger syndrome spectrum | 8 | |
| Peroxisome proliferation | PEX11 | PEXllA PEX11B PEX11G |
None | --- |
| PEX25 | None | --- | --- | |
| PEX27 | None | --- | --- |
Computational predictions added to SGD
SGD has incorporated computational GO annotations for S. cerevisiae proteins from the GO Annotation (GOA) project at EBI. These annotations are identified by the 'Annotation Method: Computational' and the evidence code 'IEA' on both the GO evidence and references page and the GO term page. To better present these annotations, slight changes have been made in the formats of the Locus Summary Page (e.g. TPS1), the GO evidence and references page (e.g. TPS1) and the GO term page (e.g. spindle pole body). In addition, the annotation method formerly called 'Core' is now called 'Manually curated' to better describe the process used to make these GO annotations. Annotations assigned from published literature (Manually curated and High-throughput) will continue to be the primary set of GO annotations for S. cerevisiae gene products. Computational annotations are not queried by the GO Term Finder and GO Slim Mapper tools, nor are they included in SGD's gene_association.sgd file containing GO annotations for S. cerevisiae gene products.
For more information on SGD's incorporation of computational GO annotations, see the publication by Hong et al., 2007
New links added: GI numbers, Ortholog resources, an organelle database, and a new microarray search tool
- NCBI protein GI numbers (GenInfo identifiers) have been added to the "All Associated sequences" option of the "Retrieve Sequences" pulldown menu for all verified and uncharacterized protein-coding locus pages. The GI identifiers are hyperlinked to NCBI's protein pages. The NCBI protein GI identifiers are also listed in the dbxref.tab file, on SGD's FTP site. For more information about NCBI protein GI identifiers, please see the Sequence Identifiers documentation at NCBI.
- Links to the Fungal Orthogroups Repository have been added to the "Comparison Resources" pulldown menu on the Locus Summary pages of 5,780 protein-coding genes. The Fungal Orthogroups Repository is a database of orthology groups among protein-coding genes of 17 Ascomycete fungi, maintained by the Regev group at the Broad Institute, MIT. Orthology groups were determined by the SYNERGY method, as described in the publication Wapinski et al., 2007.
- Ortholog Search (P-POD) links have been added to the "Comparison Resources" pulldown menu for all protein-coding locus pages. These links lead to ortholog family pages at the Princeton Protein Orthology Database (P-POD) developed by the Genome Databases Group at Princeton. The P-POD resource displays families of predicted orthologs from selected organisms, with an emphasis on providing information about disease-related genes and experimental confirmation of orthology from the literature. For more information on P-POD, see the recent publication by Heinicke et al., 2007.
- Organelle DB links have been added to the "Localization Resources" pulldown menu on the Locus Summary pages of 2,279 protein-coding genes. Organelle DB, established by the Kumar lab at the LIfe Sciences Institute, University of Michigan, contains localization information and images for this set of S. cerevisiae proteins as well as protein localization data for 138 eukaryotic organisms, with an emphasis on the constituents of organelles and protein complexes. Organelle DB is described in Wiwatwattana et al., 2007. Links will be added to additional SGD Locus Summary pages as more localization information is added to Organelle DB.
- Links to the SPELL (Serial Pattern of Expression Levels Locator) resource have been added to the "Functional Analysis" pulldown menu on the Locus Summary pages of all open reading frames. SPELL searches large gene expression microarray compendia to identify datasets relevant to a gene or set of genes, and then identifies genes in those datasets whose expression is similar to that of the query set. SPELL is described in Hibbs et al., 2007
Antibodies list started in Wiki
Periodically, SGD curators are asked if we know of a resource that lists antibodies that recognize S. cerevisiae proteins. In response, we have created a page in theCommunity Wiki to allow uses to generate this resource. An Antibodies list has been started; it is linked from the Reagents section of the wiki. Please add information about antibodies to this list by clicking the "edit" ink at the top of the page.
SGD respect your privacy
In response to concerns about displaying email addresses, the Colleague Submission and Update forms have been updated to allow you to choose whether or not your email address is displayed on your colleague page. If you do not want your email address shown, click "N" in the option provided on the form.
81 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 (August - October 2007), new summary paragraphs for the following 81 features have been added to their respective Locus Summary pages.
List of Summary Paragraphs Added During the Last Quarter
3 Sequence/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 (August - November 2007), annotation changes were made affecting 3 features and 0 new features were added.
| Chromosome | Sequence/Annotation Changes | New Features Added |
|---|---|---|
| I | None | None |
| II | None | None |
| III | MSH3/YCR092C | None |
| IV | None | None |
| V | None | None |
| VI | None | None |
| VII | None | None |
| VIII | None | None |
| IX | None | None |
| X | None | None |
| XI | YKR005C | None |
| XII | None | None |
| XIII | None | None |
| XIV | LSM7/YNL147W | None |
| XV | None | None |
| XVI | None | None |
| Mito | None | None |
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
- 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
- 6th International Meeting on Yeast Apoptosis
- Leuven, Belgium
- April 30 - May 4, 2008
- Abstract Deadline: February 1, 2008
- 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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