SGD Quarterly Newsletter, Fall 2006

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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.

Contents

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.

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!

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.

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.

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


List of Sequence Annotation Changes
I 2 ARS elements 3 ARS elements
II LSR1 14 ARS elements
III 4 ARS elements None
IV I ARS element 28 ARS elements
V 10 ARS elements None
VI None None
VII RPL26B/YGR034W 19 ARS elements
VIII I ARS element 8 ARS elements
IX I 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, I ARS element 14 ARS elements
XVI None 19 ARS elements
Mito None None

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.

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.

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 gridadmin@mshri.on.ca.

Search SGD Using 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.

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 (yeast-curator@yeastgenome.org) and we will be happy to mail them to you. This pamphlet can also be downloaded from SGD's Help Resources page.

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

Community News

  • The Gene Ontology Consortium began publishing a newsletter to highlight significant improvements and changes to the ontologies, annotations, and software that are developed by members of the GO Consortium. This newsletter will be sent to those subscribed to the GO Friends mailing list on a quarterly basis. The current newsletter highlights a paper by Reguly et al., 2006 in which the authors made use of GO to evaluate interactions and networks.
  • The IntAct team at EBI has been involved in developing guidelines for effectively reporting molecular interaction data. These guidelines are referred to as the Minimum Information required for reporting a Molecular Interaction experiment (MIMIx). A paper describing MIMIx is available on the Nature Biotechnology (NBT) website for community-review prior to publication. Please send your comments concerning this paper to NBT (biotech@natureny.com).

Upcoming Conferences and Courses

Information on registration and abstract deadlines for the following conferences is available at: http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

  • American Society of Cell Biology (ASCB)
San Diego, CA
December 9-13, 2006
  • Experimental Biology Annual Meeting
Washington, DC
April 28 - May 2, 2007
  • XXIIIrd International Conference on Yeast Genetics and Molecular Biology *
Melbourne, Australia
July 1 - July 6, 2007


asterisks indicate attendance by SGD.*

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