SGD Quarterly Newsletter

Posted November 1, 2006

In this issue:

  1. New Paper on S288C Genome Annotation and Sequence Change
  2. SGD Requests Feedback on Phenotype Information
  3. Updated Regulatory Regions in Genome Browser
  4. New Protein Pages and Proteome Browser
  5. Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae
  6. New ARS Data Added
  7. New Cell Cycle Transcription Profiles Available
  8. BioGRID version 2.0.20 released (866 physical and genetic interactions added)
  9. Search SGD Using Other Database Identifiers
  10. SGD Quick Reference Guide Available
  11. New Summary Paragraphs for 60 Genes
  12. Community News
Manage your Newsletter Subscription

About this Newsletter

This is the November 2006 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.

  1. New Paper on S288C Genome Annotation and Sequence Change

    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.

  2. SGD Requests Feedback on Phenotype Information

    We are in the process of collecting and curating more comprehensive and referenced information about mutant phenotypes. As we develop new ways to display phenotype information and new ways to search it, we would like to ask for your feedback. Please send us your comments about:

      - the type of phenotype information you'd like to see in SGD
      - the types of searches you'd like to do
      - ways in which phenotype information should be integrated with existing SGD tools (for instance, should it be a criterion for the Advanced Search? should the Quick Search look at the text of phenotypes?)

    We appreciate your help in developing SGD!

  3. Updated Regulatory Regions in Genome Browser

    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.

  4. New Protein Pages and Proteome Browser



    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 (pictured above) and 'Protein Info & Structure' pull-down 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.

  5. Sequence and Annotation Changes Made to the Systematic Sequence of S. cerevisiae

    As new data become available, SGD curators update the systematic sequence and its annotation. During the last quarter, sequence and/or annotation changes were made affecting 37 features and 172 new features were added, listed in the table below. More detailed 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.

    List of Sequence/Annotation Changes
    ChromosomeSequence/Annotation Changes New Features Added
    I 2 ARS elements 3 ARS elements
    II LSR1 14 ARS elements
    III 4 ARS elements None
    IV 1 ARS element 28 ARS elements
    V 10 ARS elements None
    VI None None
    VII RPL26B/YGR034W 19 ARS elements
    VIII 1 ARS element 8 ARS elements
    IX 1 ARS element 8 ARS elements
    X HSP150/YJL159W, 7 ARS elements None
    XI None 13 ARS elements
    XII MRPL15/YLR312W-A 16 ARS elements
    XIII None SNR86/snR86, 17 ARS elements
    XIV 3 ARS elements 12 ARS elements
    XV MGM1/YOR211C, DCS2/YOR173W, MDH2/YOL126C, 1 ARS element 14 ARS elements
    XVI None 19 ARS elements
    Mito None None

  6. New ARS Data Added

    SGD has incorporated 171 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. See the 'Annotation Changes' section of the Chromosome History pages for more information. A link to OriDB, the DNA replication Origin DataBase, has also 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.

  7. New Cell Cycle Transcription Profiles Available

    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.

  8. BioGRID version 2.0.20 released (866 physical and genetic interactions added)

    The curated set of protein and genetic interactions described in Reguly et al., 2006 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 .

  9. Search SGD Using Other Database Identifiers

    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.

  10. SGD Quick Reference Guide Available

    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.

  11. New Summary Paragraphs for 60 Genes

    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 60 genes have been added to their respective Locus Summary pages.

    Summary Paragraphs Added During the Last Quarter
    ADH6/YMR318C ADH7/YCR105W APN1/YKL114C APN2/YBL019W ASF1/YJL115W BAT1/YHR208W
    BAT2/YJR148W CDC28/YBR160W COQ2/YNR041C COX1/Q0045 COX12/YLR038C COX13/YGL191W
    COX2/Q0250 COX3/Q0275 COX4/YGL187C COX5A/YNL052W COX5B/YIL111W COX6/YHR051W
    COX7/YMR256C COX8/YLR395C COX9/YDL067C CSM4/YPL200W ENA1/YDR040C ENA2/YDR039C
    ENA5/YDR038C FLP1/R0010W FLX1/YIL134W GAL1/YBR020W GAL10/YBR019C GAL2/YLR081W
    GAL3/YDR009W GAL7/YBR018C GAL80/YML051W HEM1/YDR232W HOG1/YLR113W HPT1/YDR399W
    KTI12/YKL110C LEU1/YGL009C LEU4/YNL104C LEU5/YHR002W LEU9/YOR108W MET1/YKR069W
    MSH1/YHR120W MSH2/YOL090W MSH3/YCR092C MSH6/YDR097C MYO1/YHR023W MYO4/YAL029C
    PFK1/YGR240C PFK2/YMR205C RAD18/YCR066W RAF1/R0030W REP1/R0020C REP2/R0040C
    SIN3/YOL004W TOS3/YGL179C WHI3/YNL197C WHI5/YOR083W XPT1/YJR133W YHC3/YJL059W

  12. Community News

Manage your Newsletter Subscription

If you think friends or colleagues would be interested in receiving this newsletter, they can subscribe by filling out an SGD colleague form and selecting 'Y' to become an SGD contact. The form can be found using this URL:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch.

If you are receiving this newsletter by email and do not want to continue your subscription, you may indicate this by changing the preference for the question "Do you want to be a contact for SGD (receive quarterly newsletters)?" from 'Y' to 'N' on your colleague form accessible at:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch.

As always, please contact SGD with any comments or suggestions at: yeast-curator@yeastgenome.org
Return to SGD Send a Message to the SGD Curators