What's New in SGD in 2006

December 19, 2006

• A new microarray dataset, "Transition from fermentative to glycerol-based respiratory growth" has been added to Expression Connection (Roberts et al 2006). This study measures the expression of S. cerevisiae genes during a shift from glucose-based fermentative conditions to glycerol-based respiratory conditions. Thanks to George Roberts for assistance in checking and loading the data.

December 13, 2006

• SGD has made several changes to Gene Ontology resources
• Introduction of the Annotation Type concept to distinguish annotations made from experiments focusing on specific genes, the (Core) set, versus those derived from a high-throughput approach, (High-throughput) annotations. GO annotations are labelled as Core or High-throughput on the Locus Summary page, GO Evidence and References page, and the Term Details page.
• The GO Term Finder tool has been updated to include several new functionalities. This tool now allows you to filter the background set based on feature type (protein, tRNA, etc.), feature qualifier (verified, uncharacterized, dubious), annotation type (core, high-throughput), or the GO evidence code (IMP, IDA, IGI, etc.) of the annotation.
• The GO Slim Mapper tool has been updated to allow filtering by annotation type (Core, High-throughput)
• The Gene Ontology Consortium (GOC) recently merged the three 'unknown' terms, biological_process unknown(GOID:0000004), molecular_function unknown (GOID:0005554) and cellular_component unknown (GOID:0008372) in the three ontologies to their respective root terms biological process (GOID:0008150), molecular function(GOID:0003674) and cellular function (GOID:0005575) to improve the ability to do computational reasoning on the ontology. SGD has updated its annotations to reflect this change. We have modified the display of the root terms to help make it clear that annotation to the root nodes indicates lack of knowledge at the time the annotation was made.

December 8, 2006

• The distribution of RNA polymerase II (Pol II) across the S. cerevisiae genome reported in Steinmetz, et al. (2006) Mol Cell 24(5):735-746 can be viewed in Genome Browser. To see this data, you may need to check the "Pol II distribution - Steinmetz, et al (2006)" track and select the "Update Image" button or the red "Reset" button. The data are available from SGD's FTP site. Thanks to David Brow and Christopher Warren for working with SGD on incorporating their data.

December 6, 2006

• SGD has incorporated the 2 micron plasmid as a genomic feature and updated the annotations of the four ORFs on the plasmid (FLP1/R0010W, REP1/R0020C, RAF1/R0030W, REP2/R0040C). ORF sequences can be obtained from the individual Locus Summaries or in files on the FTP site. The sequence for the entire 2 micron plasmid can be obtained from GenBank.
• The 2 micron plasmid is also now part of SGD's S. cerevisiae BLAST Search, which has recently been updated to facilitate selection of a variety of different target sequence datasets.

December 1, 2006

• Two new microarray datasets have been added to Expression Connection: "Expression in response to anoxia (0 - 6 generations) and subsequent reoxygenation (6 - 7.6 generations) in galactose" and "Expression in response to anoxia (0 - 6 generations) and subsequent reoxygenation (6 - 7.6 generations) in glucose" (Lai et al. 2006). This study measures the expression of S. cerevisiae genes during growth under anaerobic conditions followed by a shift to aerobic conditions, using either galactose or glucose as carbon sources. Thanks to Kurt Kwast and his group for contributing their results and for assistance in checking and loading the data.
• SGD's Expression Connection allows users to search expression patterns for multiple genes across multiple microarray experiments. Datasets in Expression Connection are also available for download from SGD's FTP site.

November 20, 2006

• The Saccharomyces Genome Resequencing Project (SGRP) has sequenced 14 S. cerevisiae strains and 21 S. paradoxus strains and the data are now available at the Sanger Institute. The SGRP Genome Browser allows users to browse alignments, SNPs and annotations for the sequenced data. The strains will be available from the National Collection of Yeast Cultures (NCYC) as well as from Ed Louis' Lab. While using these data, the SGRP requests that researchers adhere to the Data Release Policy posted on their website. A link to the SGRP website is available from SGD's External Links page. The SGRP is a collaboration between the Sanger Institute and Prof. Ed Louis' group at the Institute of Genetics, University of Nottingham.

November 13, 2006

• 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 Chromosome History Search and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

On 2006-11-09, sequence changes were made affecting MET4/YNL103W.

November 13, 2006

• SGD now displays Transporter Classifications (TC) made by the Yeast Transporter Information (YETI) project, part of Genolevures (De Hertogh B, et al. (2006) Genetics 172(2):771-81). The TC numbers assigned to individual proteins are displayed in the "External Classifications" section of Protein Information pages, and links to the Transporter Classification Database (TCDB) are listed in the External Links sections of both the Locus Summary and the Protein Information pages. These assignments are also included in the dbxref.tab file on our FTP site. Many thanks to Marie-Line Renaut-Seret, Philippe Baret and Andre Goffeau for their help incorporating this information.

November 1, 2006

• 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.

October 31, 2006

• A new microarray dataset has been added to Expression Connection: "Response to creating a single unrepaired DSB by HO endonuclease in nocodazole-arrested cells" (Lee et al. 2000). This study measures the expression of S. cerevisiae genes during arrest, adaptation, and recovery following a chromosome double-strand break. Thanks to Jim Haber and Audrey Gasch for contributing their results and assistance in loading the data.
• SGD's Expression Connection allows users to search expression patterns for multiple genes across multiple microarray experiments. Datasets in Expression Connection are also available for download from SGD's FTP site.

October 18, 2006

• GBrowse has been updated to include an expanded "Regulatory regions & binding sites" section that can display data from multiple sources. To see this new display, you may need to toggle this track "All on" and then select the "Update Image" button. The first set of new data in this section was published by Tachibana, et al. (2005) and we thank Chris Tachibana and Ted Young for working with SGD on incorporating their data. If your lab has data that would be appropriate to display in this section of GBrowse, please contact SGD curators.

October 18, 2006

• Yeast has recently published a paper authored by members of SGD. Fisk, et al. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 2006 Sep; 23(12):867-65 was written in celebration of the tenth anniversary of the completion of the S. cerevisiae genome sequence and discusses the ways in which the sequence and its annotation have changed in the decade since it was first published. The changes to the systematic sequence described in this publication can also be viewed via the Chromosome History pages.

October 6, 2006

• 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 Chromosome History Search and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2006-10-02 and 2006-10-06, sequence and/or annotation changes were made affecting 7 features (HSP150/YJL159W, LSR1, RPL26B/YGR034W, MRPL15/YLR312W-A, MGM1/YOR211C, DCS2/YOR173W, and MDH2/YOL126C) and one new feature was added (SNR86/snR86).

September 15, 2006

• SGD has incorporated new ARS elements with confirmed replication origin activity from Nieduszynski et al. 2006, greatly increasing the number of S. cerevisiae replication origins represented in SGD. A link to OriDB, the DNA replication Origin DataBase, has been added to SGD's External Links resource. Many thanks to Conrad Nieduszynski and Anne Donaldson at the University of Aberdeen for providing the data.

September 14, 2006

• We have enhanced the depth and accessibility of protein information at SGD through the redesign of the Protein Information page, the Domains/Motifs page, and through the introduction of a Physico-chemical Properties page. These resources are available via the 'Protein' tab and 'Protein Info & Structure' pulldown menu on all Locus Summary pages. Inter-page navigability is also possible through the use of sub-tabs, located at the top of all Protein Information pages. In addition, a GBrowse-derived interactive Proteome Browser has also been introduced to enhance the visualization of protein sequence-based information. Thumbnail images available on all Protein Information and Domains/Motifs pages provide a point of entry to this interactive browser designed to consolidate the display of domains/motifs (InterPro), transmembrane regions (TMHMM), signal peptides (SignalP), and hydropathy plots.

Please clear your browser's cache, located in either the preference or tools menu, if you are unable to view these changes.

August 23, 2006

• A link to cell cycle transcription profiles has been added to the Functional Analysis pull-down menu on Locus Summary pages for all systematically named ORFs. These profiles were created based on the work of Pramila et al., 2006, who assayed alpha-factor synchronized cells for expression across the cell cycle using spotted cDNA arrays, and analyzed the results in conjunction with public domain data sets. In addition, an interactive resource entitled Periodic Genes of the Yeast Saccharomyces cerevisiae can be accessed in the Expression Data Resources section of the External Links page. Thanks to Linda Breeden and William Noble for generating the expression profile summary pages.

August 23, 2006

• The BioGRID version 2.0.20 release (866 physical and genetic interactions added) has been added to SGD. The curated set of protein and genetic interactions described in Reguly et al. (Journal of Biology, 2006, 5:11) has been updated from the period November 1, 2005 to May 1, 2006, to include an additional 866 protein and genetic interactions; these data are available over the web and via bulk download through both BioGRID and SGD. This additional dataset brings the total number of literature curated interactions to 34,177. New interactions will be added in curation updates on a monthly basis, and these updated data will be available in both SGD and BioGRID. Please let us know of any missed or incorrectly reported interactions by sending an e-mail to .

August 18, 2006

• S. cerevisiae genes or proteins can now be retrieved in SGD using UniProt IDs, E.C. numbers, GenBank/EMBL/DDBJ accession IDs, and NCBI Gene IDs. For example, the Locus Summary page for LEU2/YCL018W can be accessed by entering the E.C. number 1.1.1.85 or UniProt ID P04173 in the Quick Search. Accession IDs from NCBI and UniProt are updated weekly from the NCBI RefSeq and EMBL-EBI Genome Reviews databases. All data are available from the 'dbxref.tab' file in the chromosomal_feature/ directory on our FTP site.

August 3, 2006

• The 'SGD Quick Reference Guide' distributed at the 2006 YGMB meeting at Princeton is now available for download. This pamphlet describes the content and usage of many resources available at SGD. If you would like to receive hard copies of this pamphlet, please contact SGD and we will be happy to mail them to you. This pamphlet can also be downloaded from SGD's Help Resources page.

July 10, 2006

• The SGD full-text literature search capability (powered by Textpresso) has been expanded, and now includes 44,000 yeast-related full-text journal articles. The full-text literature search can be accessed via the Full-text search link on the home page, from a link on the SGD Search Options contents page, and from the Literature pulldown menu on the right side of all Locus Summary pages, where the search form is prefilled with the ORF or gene name.

June 23, 2006

• SGD has implemented new Chromosome History pages, which display the complete sequence and annotation history of each chromosome since the initial release of the systematic reference sequence on 1996-07-31. Chromosome Histories can be accessed through the Chromosome History Search via the Sequencing Tables link at the bottom left of the homepage under Download Data.

June 16, 2006

• SGD has added data to its FTP site (systematic_results directory) from Kastenmayer JP et al. (2006), a study that describes the phenotypes of gene-deletion mutants of 247 small open reading frames (sORFs) in S. cerevisiae. These deletion strains are available as supplemental sets from [Open Biosystems].

June 2, 2006

• The transcription factor binding sites published by Harbison, et al. (2004) have been remapped to the current S. cerevisiae genome sequence. These data can be viewed in GBrowse and in the "Regulatory Role" section on the Locus Summary pages (see SUM1). In addition, the regulatory map data from MacIsaac, et al (2006) are available from the FTP site. Thanks to Kenzie MacIsaac for providing information to remap the binding sites and new data to SGD.

May 12, 2006

• As new data become available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found in the Table of Sequence Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2006-04-15 and 2006-05-12, sequence and/or annotation changes were made affecting 16 features (UTR4/YEL038W, YJR003C, YKL207W, KKQ8/YKL168C, CAF4/YKR036C, SEN15/YMR059W, ZIM17/YNL310C), SPS19/YNL202W, MCA1/YOR197W, CEN1, CEN4, CEN5, CEN6, CEN7, CEN9, and CEN16).

May 1, 2006

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

April 19, 2006

• Links to eukaryotic OrtholoGY (YOGY), a tool to view orthologous proteins from eukaryotic organisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae), have been added to the Model Organism BLASTP Best Hits page and the Comparison Resources pull-down menu on the Locus Summary pages. This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL, and manually curated orthologs between S. cerevisiae and S. pombe. YOGY was developed by Penkett CJ, Morris JA, Wood V, and Bahler J (Wellcome Trust Sanger Institute, Cambridge, UK).

April 14, 2006

(As new data becomes available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found in the Table of Sequence Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2006-04-10 and 2006-04-14, sequence and/or annotation changes were made affecting 7 features (ARS416 (aka ARS1), ARS808 (aka ARS2), RRI1/YDL216C, MGT1/YDL200C, PEX19/YDL065C, YDR015C, SIP1/YDR422C) and 7 new features were added (ARS404, ARS422, ARS1516, ARS706, ARS1208, ARS805, and HED1/YDR014W-A).

April 13, 2006

• SGD has expanded our literature curation procedures to better annotate papers that describe the biology of S. cerevisiae without investigating the function(s) of specific gene(s). In order to capture the range of topics addressed in these papers, the following new Literature Topics have been added to the Literature Guide: Cell growth and Metabolism, Infection and Antifungals, Industrial Applications, Evolution, and Nucleic Acid Interaction. Papers grouped according to these new and existing Literature Topics are accessible from the SGD Curated Paper page for any reference in SGD. For example, clicking on the green ball of the curated paper page for Henry, et al. retrieves a list of all references curated for the topic "Infection and Antifungals".

April 7, 2006

• SGD has joined with BioGRID (Stark et al.) to provide a common dataset of budding yeast interactions. More than 65,000 genetic and physical interactions are now available from SGD. This dataset is described by Reguly et al., Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces cerevisiae, Journal of Biology, in press. SGD, BioGRID and the SGD Colony at Princeton are working together to maintain and update this complete dataset of yeast genetic and physical interactions. We thank Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark for their help in providing and loading the data.

April 5, 2006

• We regret that many of the coordinates previously listed for transcription binding sites were incorrect because the data were not synchronized to the current version of the genome. As a result, many coordinates were offset due to upstream insertions or deletions in the reference sequence. We are updating these data, and they will be re-released when they are properly synchronized. We apologize for any confusion or inconvenience that this may cause.

March 31, 2006

• A set of files detailing the sequence and location of every palindrome in the S. cerevisiae genome has been added to SGD's FTP site. The data were generated in a study published by Lisnic, B., et al. Many thanks to Berislav Lisnic for contributing the results and for assistance with the files.

March 7, 2006

• SGD has added the data from Myers et al (2005) Genome Biol 6:R114, a study that describes a novel system for data integration and visualization, to the SGD FTP site. In addition, links are provided to the accompanying BioPIXIE tool, which allows you to search and visualize interaction networks involving your gene(s) of interest; these links can be found on all SGD Locus Summary pages within the Interactions pull-down menu on the right side of the page. Thanks to Chad Myers in Olga Troyanskaya's lab for providing this information to SGD.

March 7, 2006

• As new data becomes available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found in the Table of Sequence Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly.

Between 2006-01-26 and 2006-03-03, one existing feature was merged with an overlapping ORF (YLR312C-B), and 4 new features were added (ARS110, ARS209, ARS600, and SNR87).

March 1, 2006

• The Batch Download tool has been updated to allow simultaneous retrieval of data for features from several chromosomes or chromosomal regions. A file specifying chromosomal regions or simply chromosome numbers may now be uploaded on this interface to retrieve different types of data for the features included in the chromosomal regions or chromosomes. The Batch Download tool can be accessed through links on the Analysis & Tools and Download Data contents pages.

February 17, 2006

• The SAGE data published by Velculescu et al. (1997) have been remapped to the recently updated S. cerevisiae systematic sequence. SAGE tags can be displayed in the ORF Map and by selecting the "SAGE tags" track option in GBrowse (Genome Browser). The scerevisiae_sage.gff file and corresponding README are available from our FTP site.

February 14, 2006

• A new microarray data set, "Expression in response to peroxisome induction and repression" (Smith et al. 2002), has been added to Expression Connection. This study compares the expression of each S. cerevisiae gene during metabolic shifts that either induce or repress peroxisome assembly and proliferation to identify genes involved in peroxisome biogenesis or function. We thank John Aitchison and Jennifer Smith for contributing their results and assisting us in loading the data.
• 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. In order to provide a better representation of expression ratios over an increasing number of experiments, the Expression Summary histogram has recently been modified for finer binning. Data sets in Expression Connection are also available for download from the SGD ftp site.

February 2, 2006

• SGD has sent out the quarterly newsletter to colleagues designated as contacts in SGD. This issue of the newsletter is in a new format and an expanded HTML version is also available. If you have any comments or suggestions on this new format, or any other subject, please send them to yeast-curator@yeastgenome.org. If you would like to receive this letter by email in the future, please use the Submission/Update form to let us know.

January 6, 2006

• Over the course of the next several months, SGD curators will be updating the systematic sequence to correct verified errors in sequencing and/or annotation. The files on our ftp site will be updated on a weekly basis. Comprehensive information about changes to the systematic sequence can be found in the Table of Sequence Updates. Sequence/annotation change details are also described in the "Locus History" pages for affected features.
• Between 2006-01-01 and 2006-01-05, sequence and/or annotation changes were made affecting 2 features (TMA16/YOR252W and FRE7/YOL152W).
• Between 2006-01-09 and 2006-01-13, sequence and/or annotation changes were made affecting 6 features (YCL025C, YCL058W-A, REC102/YLR329W, DUS3/YLR401C, AI3/Q0060, and AI4/Q0065)
• Between 2006-01-17 and 2006-01-20, sequence and/or annotation changes were made affecting 4 features (JJJ2/YJL162C, ASG7/YJL170C, RRP8/YDR083W, and SWH1/YAR042W).
• Between 2006-01-23 and 2006-01-26, sequence and/or annotation changes were made affecting 3 existing features (RHR2/YIL053W, CBR1/YIL043C, and CTT1/YGR088W) and 3 new features were added (snR81, snR85, and RNA170).

January 1, 2006

• The 2006 Nucleic Acids Research Database issue is now available. This issue includes a paper (HTML|PDF) by the SGD staff describing the new [Genome Snapshot] tool at SGD. (Posted January 1, 2006)