Kyla at 22:41, 19 December 2013

2013-12-19T22:41:07Z

Kyla at 22:37, 19 December 2013

2013-12-19T22:37:25Z

Kyla: Created page with "Category:Newsletter 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 fo..."

2013-12-19T17:54:52Z

Created page with "Category:Newsletter 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 fo..."

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[[Category:Newsletter]]
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.

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

==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.
==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.
==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.
==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.
==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.
==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.
==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:
{| class="wikitable"
|-
| 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 || GDH1 || MAC1 || PUT1 || TPS1
|-
| BNI4 || FRE1 || GIP2 || MEK1 || PUT2 || TPS2
|-
| BUD14 || FRE2 || GLC3 || NTH1 || PUT3 || TPS3
|-
| BUL2 || FRE3 || GLC8 || NTH2 || PUT4 || TPS3
|-
| 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

*November 12 - November 17, 2005
:Comparative Genomics of Eukaryotic Microorganisms:
:Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi
:Sant Feliu de Guixols, Spain

*November 13 - November 17, 2005
:4th International Meeting on Yeast Apoptosis
:Wyndham Miami Beach Resort, Miami, FL

*January 5 - January 7, 2006
:Genetic Analysis: Model Organisms to Human Biology
:San Diego, California

*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

 '''Manage your subscription''' 
 To SUBSCRIBE: If you think friends or colleagues would be interested in receiving this newsletter, they can subscribe by filling out an [http://www.yeastgenome.org/cgi-bin/colleague/colleagueSearch SGD colleague form], and selecting 'Y' to receive the SGD newsletter. 
 '''[http://www.yeastgenome.org/cgi-bin/suggestion CONTACT SGD]'''

@@ Line 1: / Line 1: @@
 [[Category:Newsletter]]
 <br>'''About this newsletter:'''<br \>
-This is the October 2005 issue of the quarterly SGD newsletter.  The
+<br>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.
+SGD and to foster communication within the yeast community.<br \>
 Other relevant URLs mentioned in this newsletter are also at the

SGD Quarterly Newsletter, Fall 2005 - Revision history

Kyla at 22:41, 19 December 2013

Kyla at 22:37, 19 December 2013

Kyla: Created page with "Category:Newsletter 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 fo..."