SGD Quarterly Newsletter, Summer 2003

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About this newsletter:

This is the August 2003 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.

As always, please contact SGD with any comments or suggestions at: yeast-curator@genome.stanford.edu

Contents

Reannotation of the S.cerevisiae genome

SGD has revised the current annotation of the S. cerevisiae genome. This revised annotation has two notable components:

  1. The addition of 354 ORFs, as reported in various literature including Brachat et al. (Genome Biol (2003) 4(7):R45), Kessler et al. (Genome Res (2003) 13(2): 264), Kumar et al. (Nat Biotechnol (2002) 20(1):58), and Oshiro et al. (Genome Res 12(8):1210).
  2. The classification of all ORFs, as "Verified", "Uncharacterized", or "Dubious", according to the degree of certainty that each ORF actually encodes a protein. These classifications were made based on three large scale comparative :genomics studies (Cliften et al. (Science (2003) 301:71) and Kellis et al. (Nature (2003) 423: 241 and Brachat et al. (Genome Biol (2003) 4(7):R45)) and our own survey of available literature.

SGD considers this a working hypothesis and welcomes input from the yeast community on these classifications.

Easier URL (www.yeastgenome.org)

SGD has migrated to a new URL that is easier to remember and quicker to type. If you bookmarked our old URL you will be redirected to our new URL.

Fungal sequences from Cliften et al. and Kellis et al. and alignment tools available at SGD

Genomic sequence data from Saccharomyces sensu stricto and sensu lato species, as published by Cliften et al. (Science (2003) 301:71) and Kellis et al. (Nature (2003) 423: 241), can now be viewed on the web and aligned with S. cerevisiae sequences at SGD. The Fungal alignment viewer can be accessed from the locus page or from the 'Homology and Comparisons' link from SGD's home page. These sequences are also available for download at SGD's ftp site.

Yeast Biochemical Pathways

This is a new resource at SGD for viewing and searching biochemical reactions and pathways that occur in S. cerevisiae. The Yeast Biochemical Pathways tool, which can be accessed by clicking the 'Function and Expression' link on SGD's home page, offers:

  1. a query page to search for pathways, enzymes, reactions, compounds etc.
  2. a metabolic map which gives a 'bird's eye view' of S. cerevisiae metabolism
  3. Expression viewer, a tool to overlay expression data on the metabolic map

Pathways in which a gene product functions are displayed on its locus page, beneath the Gene Ontology annotations; clicking on the pathway name leads to a page showing the pathway in diagrammatic form. This information is also available for download at the ftp site. These pathway representations are created and edited using the Pathway Tools software developed and maintained by Peter Karp and his colleagues at SRI International but the content is reviewed and updated by SGD.

New Regulatory module information in Expression Connection

Expression Connection, SGD's tool for querying microarray datasets, has added results of computational analyses published by Segal et al. (Nat Genet., (2003), 34:166) that predict regulatory modules for clusters of genes whose expression seems to be coordinately regulated under different conditions. This information is available for Spellman et al. (Mol Biol Cell (1998), 9(12):3273) and Gasch et al. (Mol Biol Cell (2001), 12(10):2987) and can be viewed by clicking on the red "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.

Predicted signal peptide cleavage sites and transmembrane domains available on Protein Info page

Predicted signal peptide cleavage sites and transmembrane domains are available on the Protein Info page. These features are predicted using EMBOSS software. The Protein Info page for any gene/ORF can be accessed from the locus page or by following the links under 'Function and Expression' from SGD's home page.

Email requests for Community Annotations

Since July 22, 2003 SGD has been sending emails to the corresponding authors of recently published yeast related papers requesting submissions of Community annotations, on a weekly basis. The community annotation system was introduced by SGD to allow yeast researchers to highlight a research finding from a published paper about a gene or protein. This will allow SGD to collect and display important findings from yeast literature.

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

  • August 12-17, 2003: Yeast Cell Biology meeting at Cold Spring Harbor, New York.
  • August 27- September 1, 2003: II International Conference on Molecular Mechanisms of Fungal Cell Wall Biogenesis at Salamaca, Spain.
  • August 29-September 1, 2003: 21st Small Meeting on Yeast Transport & Energetics (SMYTE) at Bonn, Germany.
  • September 17-20, 2003: The International Meeting on Yeast Apoptosis at the Smolenice castle, Slovak Republic.
  • October 16-17, 2003: Biology in the Post-Genomic Era, 4th Colmar Scientific Symposium at Colmer, France.
  • August 7-25, 2003: Course on Molecular Mycology: Current Approaches to Fungal Pathogenesis at Woods Hole, MA, U.S.A.


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