SGD Quarterly Newsletter

Posted July 30, 2007

In this issue:

  1. Transcription Data in Genome Browser
  2. How Many Uncharacterized Yeast Genes?
  3. Links to Protein, Strain, and Expression Websites Added
  4. Improvements to SGD software
  5. New Summary Paragraphs
  6. Annotation Changes Made to the Systematic Sequence of S. cerevisiae
  7. Upcoming Conferences and Courses
Manage your Newsletter Subscription

About this Newsletter

This is the July 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.

  1. Transcription Data in Genome Browser

    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.

  2. How many Uncharacterized yeast genes?

    Hughes & Pena-Castillo's paper, 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.

  3. Links to Protein, Strain, and Expression Websites Added

  4. Improvements to SGD software

    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.

  5. 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 (May - July 2007), new summary paragraphs for the following 159 features have been added to their respective Locus Summary pages.

    List of Summary Paragraphs Added During the Last Quarter
    AGC1/YPR021C BCY1/YIL033C CDC13/YDL220C CDC34/YDR054C CMD1/YBR109C
    COB/Q0105 COR1/YBL045C CYR1/YJL005W CYT1/YOR065W DNL4/YOR005C
    EST1/YLR233C EST2/YLR318W EST3/YIL009C-A FKS1/YLR342W FKS3/YMR306W
    FUS3/YBL016W GAS1/YMR307W GAS2/YLR343W GAS3/YMR215W GAS4/YOL132W
    GAS5/YOL030W GPA1/YHR005C GSC2/YGR032W HHO1/YPL127C HSP26/YBR072W
    HSP42/YDR171W HTA1/YDR225W HTA2/YBL003C KSS1/YGR040W LIF1/YGL090W
    MLH2/YLR035C MLH3/YPL164C PAC1/YOR269W PDC1/YLR044C PDC5/YLR134W
    PDC6/YGR087C PEX1/YKL197C PEX2/YJL210W PEX3/YDR329C PEX5/YDR244W
    PEX6/YNL329C PEX7/YDR142C PEX10/YDR265W PEX12/YMR026C PEX13/YLR191W
    PEX14/YGL153W PEX17/YNL214W PEX18/YHR160C PEX19/YDL065C PEX21/YGR239C
    PMS1/YNL082W POL30/YBR088C PRC1/YMR297W QCR2/YPR191W QCR6/YFR033C
    QCR7/YDR529C QCR8/YJL166W QCR9/YGR183C QCR10/YHR001W-A RAD26/YJR035W
    RIP1/YEL024W RPS19A/YOL121C RPS19B/YNL302C SCS2/YER120W SCS22/YBL091C-A
    SDP1/YIL113W SPO11/YHL022C SST2/YLR452C SUC1/SUC1 SUC2/YIL162W
    SUC3/SUC3 SUC4/SUC4 SUC5/SUC5 SUC7/SUC7 TLC1/TLC1
    TPK1/YJL164C TPK2/YPL203W TPK3/YKL166C UGA1/YGR019W UGA2/YBR006W
    YAP1/YML007W YKU70/YMR284W YKU80/YMR106C 76 snoRNA genes

  6. 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 (May - July 2007), annotation changes were made affecting 10 RNA genes and new introns were annotated within 9 protein-coding features. 1 new feature was added.

    Chromosome Annotation Changes New Features
    I snR18, HRA1 none
    II HPC2/YBR215W none
    III none none
    IV IWR1/YDL115C none
    V GIM4/YEL003W none
    VI none none
    VII snR46 none
    VIII PTC7/YHR076W none
    IX none none
    X snR3 none
    XI none none
    XII snR30, snR34 none
    XIII snR78, CGI121/YML036W, RPL20A/YMR242C none
    XIV HRB1/YNL004W none
    XV snR35, snR36, RPL20B/YOR312C none
    XVI snR70, YPR153W YPR010C-A

  7. Upcoming Conferences and Courses (*asterisks indicate attendance by SGD)

Manage your Newsletter Subscription

TO SUBSCRIBE: If you think friends or colleagues would be interested in receiving this newsletter by email, they can subscribe by filling out an SGD colleague form, found using this URL:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch.

TO UNSUBSCRIBE: 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 quarterlynewsletters)?:Y/N "
on your colleague form also accessible at:
http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch.

CONTACT SGD: yeast-curator@yeastgenome.org
Return to SGD Send a Message to the SGD Curators