What's New in SGD in 2007

December 20, 2007

• SGD has updated the Yeast GO Slims, the Macromolecular Complex GO Slim data sets and the go_slim_mapping.tab file on the FTP site. The Yeast GO Slims are a set of high-level GO terms that best represent the major biological processes, molecular functions, and cellular components that are found in S. cerevisiae. GO Slim terms are useful in mapping precise, "granular" gene annotations to more general "high-level" terms. These terms have been selected by SGD curators based on annotation statistics and biological significance.
• Six new terms were added to the Yeast Biological Process GO Slim and two to the Yeast Molecular Function GO Slim. The Yeast GO Slims are available for analysis via the GO Slim Mapper tool and the Advanced Search tool. Mapping of all the yeast gene products to the Yeast GO Slims is also available as a graphical view on the Genome Snapshot page and via the go_slim_mapping.tab file on the FTP site.
• The Macromolecular Complex GO Slim now only includes macromolecular complex terms that have been used to annotate S. cerevisiae gene products. The Macromolecular Complex GO Slim is available for analysis via the GO Slim Mapper tool and a mapping of all the yeast gene products to these Slim terms is available via the go_protein_complex_slim.tab file on the FTP site.
• Data in the go_slim_mapping.tab file on the FTP site now handles parentage in the same way as the GO Slim Mapper web interface. In contrast to previous versions of this file, annotations are now mapped to all available GO Slim terms regardless of distance to a GO Slim term.

December 14, 2007

• 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 2007-12-10 and 2007-12-13, the sequence of Chromosome VII was updated, affecting features EFG1/YGR271C-A and YGR272C; and the annotations of the mating-type loci (HML, MAT, HMR) on Chromosome III were updated.

November 28, 2007

• A new green icon has been added to references that are associated with curated genomics data sets at the Yeast Functional Genomics Database (YFGdb). YFGdb is an ongoing project to collect, curate, and disseminate all yeast functional genomics data by providing a means to view and download the data. Currently, there are links from over 450 papers in SGD to the corresponding YFGdb page. View references curated to the literature topic Genomic expression study for examples.

November 8, 2007

• SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

November 6, 2007

• The Saccharomyces Genome Resequencing Project (SGRP) has nearly finished sequencing 37 S. cerevisiae strains and 27 S. paradoxus strains. Details of the sequence analysis and publication time line are available as a PDF document. More information on this collaboration between Richard Durbin and Ed Louis can be found on their websites at the Sanger Institute and the University of Nottingham.

October 30, 2007

• 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 the Community Wiki to allow users 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" link at the top of the page.

October 3, 2007

• 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.

September 24, 2007

• Links to Organelle DB 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 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.
• 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.

September 12, 2007

• 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.

September 7, 2007

• As new data become available, SGD curators 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 2007-09-04 and 2007-09-07, annotations were updated for 3 ORFs: MSH3/YCR092C, YKR005C, and LSM7/YNL147W.

September 5, 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 S et al.
• 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.

July 30, 2007

• SGD sent out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

July 13, 2007

• Links to structural annotations for predicted domains at the Yeast Resource Center Informatics Platform 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. Thank to Chikahsi Shimoda and Yukiko Yamazaki for setting up the links.
• 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.
• As new data become available, SGD curators 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 2007-07-09 and 2007-07-13, intron annotations were updated for 9 ORFs: HPC2/YBR215W, IWR1/YDL115C, GIM4/YEL003W, PTC7/YHR076W, CGI121/YML036W, RPL20A/YMR242C, HRB1/YNL004W, RPL20B/YOR312C, and YPR153W.

June 25, 2007

• Hughes & Pena-Castillo, 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.

June 11, 2007

• The abstracts for the 23rd International Conference on Yeast Genetics and Molecular Biology in Melbourne are now available online from SGD.

May 18, 2007

• Transcription start sites reported in Zhang Z and Dietrich FS (2005) Nucleic Acids Res 33:2838 and cDNA clones reported in Miura F et al. (2006) Proc Natl Acad Sci U S A 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.

May 18, 2007

• A link 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.

May 11, 2007

• As new data become available, SGD curators 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 [http://www.yeastgenome.org/cgi-bin/locusHistory.pl "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2007-05-07 and 2007-05-11, annotation updates were made affecting 10 RNA features (snR3, snR18, snR30, snR34, snR35, snR36, snR46, snR70, snR78, and HRA1) and one new ORF was added (YPR010C-A).

May 7, 2007

• SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

May 2, 2007

• SGD has incorporated manual GO annotations for S. cerevisiae proteins from the GO Annotation (GOA) project at Uniprot. These annotations can be identified at SGD by the source, e.g., 'Uniprot', displayed on the 'Assigned By' column of the GO evidence and references page. The GO evidence and references page can be accessed by clicking on the 'Gene Ontology' tab from any Locus Summary page (e.g., please see Gene Ontology evidence and references page for RSC6). The SGD gene_associations file, which provides a complete set of manual GO annotations for S. cerevisiae, now includes these annotations made by GOA-Uniprot.

April 30, 2007

• Locus page annotation has now been expanded to include introns located in the 5'-untranslated regions (5' UTRs) of primary transcripts. The Advanced Search can be used to obtain a complete list of genes with 5' UTR introns. We thank the many researchers who generated these data and reviewed our incorporation of it, including Manny Ares, Paul Cliften, Zhihong Zhang, Kara Juneau, and Takashi Ito.

April 6, 2007

• 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.

Between 2007-04-02 and 2007-04-06, annotation updates were made affecting features snR47 and YFR045W, sequence updates were made affecting features SSA1/YAL005C and YAL004W, and LTR annotations were updated on Chromosomes II, III, IV, V, IX, X, and XII.

March 29, 2007

• Schacherer et al. identify SNPs between S288c and seven commonly used lab strains; these data are available on the SGD FTP site and can be searched and viewed online via the Yeast SNPs Browser.

March 12, 2007

• A Community wiki for information about S. cerevisiae genes, gene products, and resources is now available. The Community wiki has been pre-loaded with basic locus information from SGD as well as user annotations previously submitted through the Community Annotation pages, and we invite the research community to further develop and enhance the information on the wiki pages. Links are available in the "Additional Information" section and from the "Literature" pull-down of each Locus Summary page as well as on the Community Info contents page.

March 9, 2007

• 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.
• Between 2007-03-06 and 2007-03-09, ARS element annotations were updated on Chromosomes I, III, IV, and VI.
• Between 2007-02-06 and 2007-02-07, annotation updates were made affecting features HRA1 and YRF1-8/YOR396W, and two new ARS elements (ARS1200-1, ARS1200-2) were added.

January 29, 2007

• SGD sends out its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter is available. If you would like to receive this letter in the future please use the Colleague Submission/Update form to let us know.

January 1, 2007

• The 2007 Nucleic Acids Research Database issue is now available. This issue includes a paper (HTML | PDF) by the SGD staff describing the expanded Protein Information at SGD. (Posted January 1, 2007)