What's New in SGD in 2003

December 19, 2003

• SGD has created a new GO Slim, consisting of a set of macromolecular complex terms. To create this GO Slim set, we choose very granular protein complex terms from the cellular component ontology that would be likely to indicate a functional relationship among gene products that are co-localized to a particular term. For example, gene products that are co-localized to the ribosome are likely to share a role in protein biosynthesis. A file (go_protein_complex_slim.tab) that contains gene products mapped to these terms can be found on our ftp site. For more on GO Slim sets and the GO project in general, see the GO Tutorial at SGD.

October 31, 2003

• SGD sends its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter can be viewed here.

October 31, 2003

• SGD curators are in the process of revising the information currently associated with the Description field, for all protein-coding and non-coding RNA genes. This project will ensure that the Description, intended to be a concise summary of the function and biological context of each gene product, contains the most up-to-date information and is written in a consistent style. New Descriptions will be added to SGD gradually over the coming weeks.

October 28, 2003

• Based on the genome-wide protein localization analysis published by Huh et al. (2003) Nature 425:686-691 and protein abundance data published by Ghaemmaghami et al. (2003) Nature 425:737-741, Cellular Component GO terms have been added for 1326 ORFs that were previously annotated to "cellular_component unknown". In addition, links to the YeastGFP database are available on the pull-down menu on the right-hand side of each locus page. The complete set of localization and abundance data is available from the SGD ftp site. Thanks to Adam Carroll and the laboratories of Erin O'Shea and Jonathan Weissman for providing the data.

October 22, 2003

• SGD has added a presentation entitled "The Art of Brewing and the Biology of Lager Yeast" to the General Yeast Topics page. This presentation, which covers the brewing process, types of brewing yeasts, and yeast attributes of brewing interest, was kindly made available by Tom Pugh and David Ryder of Miller Brewing Company.

October 15, 2003

• To address questions that we occasionally receive about the availability of protein structure viewers on various platforms, we created a protein viewer resource page. This page provide information about structural data in SGD as well as programs that are available for viewing, analyzing, and manipulating protein structures.

September 23, 2003

• Based on conservation between closely related Saccharomyces species, the start site methionine codons for 77 open reading frames have been re-annotated. The numbering for both the nucleotides in the DNA coding sequence and the amino acids in the predicted protein have been changed accordingly. For more information and a complete list of the changes, please click here, for a comparison of the old and new chromosomal coordinates, please click here.

September 15, 2003

• SGD has added the following telomere annotations to the S. cerevisiae genome (for definitions, click on the feature): Telomeric Region, X Element Combinatorial Repeat, X Element Core Sequence, Y' Element, and Telomeric Repeat. The annotation of these elements included developing a standardized nomenclature; see the Telomeric Elements section of SGD Gene Nomenclature Conventions for more information. Telomeric elements can be found using the Find Chromosomal Features Search. These data, as well as many suggestions for nomenclature and presentation, were generously provided by Dave Barton and Ed J. Louis of the University of Leicester.

September 15, 2003

• SGD has created a yeast-specific GO-Slim. It contains a set of high level GO terms that best represent the major biological processes, functions, and cellular components that are found in S. cerevisiae. This 'goslim_yeast.2003' file is available for download from the Gene Ontology Consortium's ftp site. In addition, all yeast gene products (ORFs and RNAs) have been mapped to these GO-Slim terms in the 'go_slim_mapping.tab' file which is available from SGD's ftp site.

September 8, 2003

• SGD has released the Sequence Similarity Query, a resource that displays the results of a sequence analysis performed quarterly at SGD. In this analysis, every protein sequence in S. cerevisiae is used as the query sequence for PSI-BLAST analysis against NCBI's non-redundant (nr) protein dataset. Available from the Comparison Resources pull-down menu on the SGD locus pages, this resource provides a graphical summary of the PSI-BLAST results as well as options to view the alignment between the S. cerevisiae sequence and the sequences identified in the nr dataset.

August 28, 2003

• S. cerevisiae Gene Naming Guidelines were updated to incorporate changes agreed upon by the yeast community at the Cold Spring Harbor Yeast Cell Biology meeting (August 12-17, 2003).

August 4, 2003

• SGD sends its quarterly newsletter to colleagues designated as contacts in SGD. An HTML version of the newsletter can be viewed here.

July 30, 2003

• SGD revised the current annotation to the S. cerevisiae genome: 1) Added 354 ORFs, as reported in various literature including Brachat et al., 2003, Kessler et al., 2003, Kumar et al., 2002, and Oshiro et al., 2002. A complete list of these new ORFs is also available. 2) Classified all ORFs, as "Verified", "Uncharacterized", or "Dubious", according to the degree of certainty that each ORF actually encodes a protein.

July 7, 2003

• SGD added the sequence data described in Cliften et al., 2003 and Kellis et al., 2003 for download via ftp at the SGD ftp site, in a standardized format. See the README files in each directory for more information. In addition, ORF sequences and flanking regions are viewable on the web via the Fungal alignments and Synteny Viewer options under the Comparison Resources menu from the SGD locus pages.

June 16, 2003

• Abstracts of the XXIth International Conference on Yeast Genetics and Molecular Biology are made available through SGD at www.yeastgenome.org/yeast03.

June 9, 2003

• SGD added new Regulatory Module information to Expression Connection, SGD's tool for querying microarray datasets. The new information is the result of analyses by Segal et al., published in Nature Genetics. Segal and colleagues have used a computational approach to predict regulatory modules for clusters of genes whose expression seems to be coordinately regulated under different conditions. This information (currently available for 2 datasets) can be found by clicking on the "Reg" icon located next to the dataset under Searches I and III of the Expression Connection page, and by following "Regulator" links on individual results pages.

June 2, 2003

• The sequence data described in Cliften et al. and Kellis et al. are available for download via ftp at the SGD ftp site. Thanks to both groups for providing these sequences to the yeast community. Currently, the contig sequences for each species are available, and additional data will be available soon. In addition, SGD is working on providing all these data in a common format for ease in parsing these files. See the README files in each directory for more information. Note that these results are also viewable on the web via the Fungal alignments and Synteny Viewer options under the Comparison Resources menu from the SGD locus pages.

May 20, 2003

• SGD releases the Yeast Biochemical Pathways, a resource for viewing and searching biochemical reactions and pathways that occur in S. cerevisiae. The information is also available for download at the ftp site. These pathways are created and edited using the Pathway Tools software that is developed and maintained by Peter Karp and his colleagues at SRI International but the content is reviewed and updated by SGD.

May 17, 2003

• SGD moves to an easier to remember, quicker to type URL (www.yeastgenome.org). The old URLs will continue to work.

April 28, 2003

• SGD sends its second quarterly newsletter. It was sent to all colleagues designated as contacts in SGD; users can easily unsubscribe or subscribe as they wish.

April 18, 2003

• SGD releases a new Advanced Search that allows you to easily retrieve chromosomal features (ORFs, tRNAs, centromeres, etc) from the database. The Feature Search allows you to retrieve all chromosomal features of a certain type or to limit your results based on selected criteria (such as molecular weight, amino acid length, or broad categories of function, process, or cellular location). Results can be directly imported into the GO Term Finder, GO Term Mapper, or Expression Connection tools. In addition, results can be downloaded as a text file.

April 02, 2003

• SGD releases a new version of Expression Connection. The new version has more searches and users can now search with multiple gene names. Results from multiple datasets are now presented in a succinct tabular form. New kinds of data are now presented, including Pearson Correlation and Expression Graphs for each queried gene.

March 27, 2003

• The following new links have been added to the SGD locus pages:

1. link in the Phenotype section of the locus page to Open Biosystems so you can order the deletion strain of your favorite gene.
2. link to submit a BLASTP query at NCBI as a new option under the Sequence Analysis Tools menu on the right side of the locus page. (thanks to Bob Burruss for setting up the links).
3. link to the SCOP superfamily page as a new option under the Protein Info & Structure menu on the right side of the locus page (thanks to Julian Gough for setting up the links).
4. link to the Database of Interacting Proteins (DIP) as a new option under the Interactions menu on the right side of the locus page (thanks to Lukasz Salwinski for setting up the links).

March 13, 2003

• SGD now includes phenotype data from Steinmetz et al. (2002) Systematic screen for human disease genes in yeast. Nat Genet 31(4):400-4. Based on these results, SGD has two new classes of mutants: genes that exhibit a growth defect on a non-fermentable carbon source, and genes that exhibit a growth defect on a fermentable carbon source.

March 13, 2003

• SGD announces that it will award Super-bud T-shirts to 100 researchers (25/month) who contribute community annotations to SGD. Click here to see an image of the Super-bud T-shirt.

February 4, 2003

• SGD releases a community annotation tool to allow yeast researchers to enter information based on published papers into SGD. For more information on community annotations, see the help page.

January 31, 2003

• SGD sends its first quarterly newsletter, as suggested by the SGD advisory committee at the Yeast Genetics and Molecular Biology Meeting in Madison, Wisconsin, last summer. The first newsletter was sent to all colleagues designated as principal investigators in SGD; users can easily unsubscribe or subscribe as they wish. Each newsletter will be archived via HTML.

January 23, 2003

• SGD now includes GO annotations for each aspect/ontology (process, component, and function) for all named S. cerevisiae genes. All of these annotations were assigned by SGD curators; GO terms previously assigned by automated methods (evidence code: IEA) have been replaced by referenced, manually-curated annotations. GO annotations can be viewed on the locus pages at SGD and can be mined using the GO tools (GO Term Mapper and GO Term Finder) developed at SGD. For more information on GO please see the GO home page or the SGD help page for GO.

January 14, 2003

• The 2003 Nucleic Acids Research Database issue is now available. In this issue, the SGD staff wrote a paper describing new resources for protein information in SGD.

January 3-10, 2003

• Chromosomal systematic sequences of Chr I, Chr II, Chr IV, Chr VII, Chr X, Chr XI, Chr XIII, Chr XIV, and Chr XV have been recently updated by SGD. These are the results of re-sequencing of the S288c background. More details about these sequence changes can be found here.