SGD Newsletter 2005-10-24

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SGD Newsletter 2005-10-24

SGD Newsletter
October 2005

In this issue:

What's New at SGD?

1. Transcription factor data added
2. Protein domains predicted using InterProScan
3. SGD links to the Candida Genome Database
4. Enhancement to SGD Quick Search
5. New Expression Connection dataset added - glycosylation
6. Complete set of Descriptions for protein coding genes
7. New gene summary paragraphs

Community News

Relevant URLs

This is the October 2005 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. Information on how to unsubscribe is at the bottom of this
newsletter.

If you think friends or colleagues would be interested in receiving
this newsletter, they can subscribe by filling out an SGD colleague
form, found using this URL:

http://db.yeastgenome.org/cgi-bin/colleague/colleagueSearch

Other relevant URLs mentioned in this newsletter are also at the
bottom of the page. As always, please contact SGD with any comments
or suggestions at:

yeast-curator@yeastgenome.org

What's New at SGD?
==================

1. Transcription factor data added

A new "Regulatory Role" section has been added to the Locus Summaries for
many known transcriptional regulators. This section displays
DNA-binding motifs for these transcription factors and provides links
to predicted regulatory modules in which they may be involved [as
predicted by Segal et al. 2003]. DNA-binding sites for 102
transcriptional regulators [as mapped by Harbison et al. 2004] have
also been added as a "Regulatory regions and binding sites" track to
the GBrowse map viewer, and an expanded thumbnail of this viewer now
appears in the "Sequence Information" section of the Locus Summary. The
GFF file for these binding sites is available from the ftp
site. Please see the SUM1 Locus Summary for an example of the new
transcription factor data.

2. Protein domains predicted using InterProScan

SGD displays Protein Domains and Motifs predicted by comparing
S. cerevisiae protein sequences against sequences in the InterPro
Database using the InterProScan program (Quevillon et al. 2005). The
InterPro Database integrates motif and domain information from the
Prosite, PRINTS, SMART, ProDom, TIGERFAMs and PIR Superfamily
databases. Protein Domains/Motifs can be accessed from the "Locus
Summary" and "Homology and Comparisons" pages. InterProScan results
for all S. cerevisiae proteins are also available for download from
SGD's ftp site.

3. SGD links to the Candida Genome Database

The "Comparison Resources" pull-down menu (located on the right hand
side of Locus Summary Pages) now includes links between S. cerevisiae
genes and Candida albicans homologs identified at the Candida Genome
Database (CGD). Thanks to Gavin Sherlock and Martha Arnaud for
providing homology determinations using software developed by
Inparanoid.

4. Enhancement to SGD Quick Search

PubMed IDs (e.g., 15608219) and Gene Ontology (GO) IDs (e.g.,
GO:0007117) can now be entered into the Quick Search box located at
the top of most SGD pages. An exact match to a PubMed ID will display
information about how the paper is curated for the Literature Guide,
while an exact match to a GO ID will display information about the GO
term and what genes have been annotated to that GO term at SGD. Note
that the PubMed ID search only works on publications that have been
added to SGD. If you notice that SGD is missing a relevant
publication, please contact SGD curators and we will happily add it to
the database.

5. New Expression Connection dataset added - glycosylation

A new microarray dataset, "Effects of glycosylation defects on gene
expression" (Cullen et al. 2004), has been added to Expression
Connection. This study compares the expression profiles of all genes
in cells undergoing a conditional protein glycosylation defect induced
in a pmi40-101 mutant by growing cells in medium lacking mannose and
comparing to cells grown in media supplemented with mannose. A second
experiment identifies those genes whose expression in the
glycosylation mutant is dependent on the transcription factor Ste12p.

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. Datasets in Expression Connection
are also available for download from SGD's ftp site.

6. Complete set of Descriptions for protein coding genes

An effort to update the Description line for all protein coding genes
was initiated in 2003 and completed in October 2005. The Description
has a 240-character limit and is exported to files available on the
SGD ftp site as well as to GenBank RefSeq records. These clear,
concise, and up-to-date Description lines are also displayed in other
NCBI records, including BLAST results.

7. New gene summary paragraphs

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 71 genes have been added to their
respective Locus Summaries:

ABF1 CTR2 FRE8 GSY1 POL32 SCD5
ABZ1 CTR3 GAC1 GSY2 PRO1 SDS22
ACN9 DHH1 GAT1 HOP1 PRO2 SGA1
ALO1 FET4 GDB1 LEU2 PRO3 TPI1
ATH1 FIN1 GDH2 MAC1 PUT1 TPS1
BNI4 FRE1 GIP2 MEK1 PUT2 TPS2
BUD14 FRE2 GLC3 NTH1 PUT3 TPS3
BUL2 FRE3 GLC8 NTH2 PUT4 TSL1
CAR1 FRE4 GLG1 PGK1 RED1 UGP1
CAR2 FRE5 GLG2 PGM1 REF2 URE2
CAT8 FRE6 GLN3 PGM2 REG1 YGL160W
CTR1 FRE7 GPH1 PIG1 REG2

Community News
==============

Upcoming conferences (*asterisks indicate attendance by SGD)

* October 28 - November 1, 2005
Genome Informatics
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
http://meetings.cshl.edu/meetings/info05.shtml

* November 12 - November 17, 2005
Comparative Genomics of Eukaryotic Microorganisms:
Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi
Sant Feliu de Guixols, Spain
http://www.esf.org/conferences/lc05196

November 13 - November 17, 2005
4th International Meeting on Yeast Apoptosis
Wyndham Miami Beach Resort, Miami, FL
http://www.yeast-apoptosis.org/miami/

* January 5 - January 7, 2006
Genetic Analysis: Model Organisms to Human Biology
San Diego, California
http://www.gsa-modelorganisms.org/

* July 25 - July 30, 2006
2006 Yeast Genetics and Molecular Biology Meeting
Princeton University, Princeton, NJ

* July 1 - July 6, 2007
XXIIIrd International Conference on Yeast Genetics and Molecular Biology
Melbourne, Australia
http://www.yeast2007.org/

Relevant URLs
=============

For What's New items
--------------------

SGD Homepage:
http://www.yeastgenome.org

Segal et al. 2005 reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000086472

Harbison et al. 2004 reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000081155

GBrowse map viewer:
http://db.yeastgenome.org/cgi-bin/gbrowse/yeast

GFF file for transcription factor binding sites:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/scerevisiae_regulatory.gff

SGD's ftp site:
ftp://genome-ftp.stanford.edu/pub/yeast/

SUM1 Locus Summary:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sum1

Quevillon et al. 2005 reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000086795

Protein Domains/Motifs at SGD:
http://db.yeastgenome.org/cgi-bin/protein/getDomain

Homology & Comparisons at SGD:
http://www.yeastgenome.org/HCContents.shtml

Candida Genome Database:
http://www.candidagenome.org

Inparanoid:
http://inparanoid.cgb.ki.se/

Suggestion form to contact SGD curators:
http://db.yeastgenome.org/cgi-bin/suggestion

Cullen et al. 2004 reference at SGD:
http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000077085

Expression Connection at SGD:
http://db.yeastgenome.org/cgi-bin/expression/expressionConnection.pl

PMI40 Locus Summary:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=pmi40

STE12 Locus Summary:
http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ste12

Table of Gene Summary Paragraphs:
http://www.yeastgenome.org/cache/geneSummarytable.html