Kyla at 22:34, 19 December 2013

2013-12-19T22:34:15Z

Kyla: Created page with "Category:Newsletter
'''SGD Newsletter, May 2006'''

'''About this newsletter:'''

This is the May 2006 issue of the quarterly SGD newsletter..."

2013-12-19T19:53:51Z

Created page with "Category:Newsletter <big>'''SGD Newsletter, May 2006'''</big> '''About this newsletter:''' This is the May 2006 issue of the quarterly SGD newsletter..."

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[[Category:Newsletter]]
 <big>'''SGD Newsletter, May 2006'''</big> 
 '''About this newsletter:''' 
 This is the May 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. 

==Collaboation with BioGRID Makes 65,000+ Interactions Available at SGD==
SGD has joined forces with [http://thebiogrid.org BioGRID] to provide a common dataset of budding yeast interactions. More than 65,000 genetic and physical interactions are now available from SGD. This dataset is described by Reguly et al. (2006), Comprehensive Curation and Analysis of Global Interaction Networks in ''Saccharomyces cerevisiae'', Journal of Biology, in press. SGD, BioGRID and the SGD Colony at Princeton are working together to maintain and update this complete dataset of yeast genetic and physical interactions. We thank Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark for their help in providing and loading the data.
==New Topics for Expanded Literature Curation==
SGD has expanded literature curation procedures to better annotate papers that describe the biology of ''S. cerevisiae'' without investigating the function(s) of specific gene(s). In order to capture the range of topics addressed in these papers, the following new Topics have been added to the Literature Guide: Cell Growth and Metabolism, Infection and Antifungals, Industrial Applications, Evolution, and Nucleic Acid Interaction. Papers grouped according to new and existing Literature Topics are accessible from the SGD Curated Paper page for any reference in SGD. For example, clicking on the green ball of the curated paper page for [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15597729 Henry et al. (2004)] retrieves a list of all references curated for the topic "Infection and Antifungals".
==Sequence and Annotation Changes Made to the Systematic Sequence of ''S. cerevisiae''==
SGD curators have updated the systematic sequence and its annotation. Sequence and/or annotation changes were made affecting 9 features, and 11 new features have been added. Altered or new features are listed in the What's New in SGD for 2006. Details regarding these changes can be found in the Table of Sequence Updates and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. The following table lists the sequence changes made during the last quarter.

:::::: '''List of Sequence/Annotation Changes''' 
{| class="wikitable"
|-
! Chromosome !! Sequence/Annotation Changes !! New Features Added
|-
| I || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114488 ARS110]
|-
| II || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114517 ARS209]
|-
| III || None || None
|-
| IV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000029652 ARS1/ARS416], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002422 YDR015C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002830 SIP1/YDR422C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002223 PEX19/YDL065C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002359 MGT1/YDL200C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002375 RRI1/YDL216C] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000113613 HED1/YDR014W-A], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114787 ARS404], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114834 ARS422]
|-
| V || None || None
|-
| VI || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000029653 ARS600]
|-
| VII || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114845 ARS706]
|-
| VIII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000029042 ARS2/ARS808] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114849 ARS805]
|-
| IX || None || None
|-
| X || None || None
|-
| XI || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114301 SNR87/snR87]
|-
| XII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000028570 YLR312C-B], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000004305 SPH1/YLR313C] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114848 ARS1208]
|-
| XIII || None || None
|-
| XIV || None || None
|-
| XV || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000114843 ARS1516]
|-
| XVI || None || None
|-
| Mito || None || None
|}

==Batch Download Tool Improved==
The Batch Download tool has been updated to allow simultaneous retrieval of data for features from several chromosomes or chromosomal regions. A file specifying chromosomal regions or simply chromosome numbers may now be uploaded on this interface to retrieve different types of data for the features included in the chromosomal regions or chromosomes. The Batch Download tool can be accessed through links on the Analysis & Tools and Download Data contents pages.
==Links to YOGY Tool Added==
Links to eukarYotic OrtholoGY (YOGY), a tool to view orthologous proteins from eukaryotic organisms (''Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae''), have been added to the Model Organism BLASTP Best Hits page and the Comparison Resources pull-down menu on Locus Summary Pages. This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL, and manually curated orthologs between ''S. cerevisiae'' and ''S. pombe''. [http://www.bahlerlab.info YOGY] was developed by the Fission Yeast Functional Genomics Team at the [http://www.sanger.ac.uk Wellcome Trust Sanger Institute], Cambridge, UK.
==BioPIXIE Data and Links Incorporated==
SGD has added the data from [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000114197 Myers et al. (2005)], a study that describes a novel system for data integration and visualization, to the SGD FTP site. In addition, links are provided to the accompanying [http://pixie.princeton.edu/pixie/ BioPIXIE tool], which allows you to search and visualize interaction networks involving your gene(s) of interest; these links can be found on all Locus Summary Pages within the Interactions pull-down menu on the right side of the page. Thanks to Chad Myers in [http://reducio.princeton.edu/cm/node/13 Olga Troyanskaya's lab] at the [http://www.princeton.edu/genomics/ Lewis-Sigler Institute of Integrative Genomics], Princeton, NJ for providing this information to SGD.
==SAGE Data Remapped to Updated Sequence==
The SAGE data published by [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000058021 Velculescu et al. (1997)] have been remapped to the recently updated ''S. cerevisiae'' systematic sequence. SAGE tags can be displayed in the [http://www.yeastgenome.org/cgi-bin/ORFMAP/ORFmap?chr=8&beg=441327&end=462640&sage=1 ORF Map] and by selecting the "SAGE tags" track option in GBrowse (Genome Browser). The scerevisiae_sage.gff file and corresponding README are available from our FTP site.
==New Summary Paragraphs for 59 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 59 genes have been added to their respective Locus Summary Pages.

::::: '''List of Gene Summary Paragraphs Added During the Last Quarter''' 
{| class="wikitable"
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=Q0080 ATP8/Q0080] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ARP7 ARP7/YPR034W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ARP9 ARP9/YMR033W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=BLM3 UBP3/YER151C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=BLM10 BLM10/YFL007W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=CYC1 CYC1/YJR048W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=DID4 DID4/YKL002W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ECM10 ECM10/YEL030W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL83 GAL83/YER027C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GCN5 GCN5/YGR252W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GUT1 GUT1/YHL032C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GUT2#summaryparagraph GUT2/YIL155C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=KAR2 KAR2/YJL034W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=KEX2 KEX2/YNL238W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LHS1#summaryparagraph LHS1/YKL073W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MEC1 MEC1/YBR136W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MRE11 MRE11/YMR224C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=PMA1 PMA1/YGL008C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD1 RAD1/YPL022W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD6 RAD6/YGL058W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD9 RAD9/YDR217C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD10 RAD10/YML095C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD14 RAD14/YMR201C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD50 RAD50/YNL250W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD53 RAD53/YPL153C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RTT102 RTT102/YGR275W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SIP1 SIP1/YDR422C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SIP2 SIP2/YGL208W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SIR2 SIR2/YDL042C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF1 SNF1/YDR477W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF2 SNF2/YOR290C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF4#summaryparagraph SNF4/YGL115W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF5 SNF5/YBR289W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF6 SNF6/YHL025W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF7 SNF7/YLR025W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF8 SNF8/YPL002C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF11 SNF11/YDR073W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SNF12 SNF12/YNR023W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSA1 SSA1/YAL005C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSA2 SSA2/YLL024C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSA3 SSA3/YBL075C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSA4 SSA4/YER103W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDL229W SSB1/YDL229W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSB2 SSB2/YNL209W] || SSC1/YJR045C || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSE1 SSE1/YPL106C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSE2 SSE2/YBR169C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSQ1 SSQ1/YLR369W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SSZ1 SSZ1/YHR064C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SWI1 SWI1/YPL016W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SWI3 SWI3/YJL176C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SWP82 SWP82/YFL049W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TAF14 TAF14/YPL129W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=VPS20 VPS20/YMR077C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=VPS24 VPS24/YKL041W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=VPS25 VPS25/YJR102C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=VPS36 VPS36/YLR417W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=XRS2 XRS2/YDR369C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YME2 YME2/YMR302C] ||
|}
==New Datasets Added==
#A set of files detailing the sequence and location of every palindrome in the ''S. cerevisiae'' genome has been added to SGD's FTP site. The data were generated in a study published by [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000081088 Lisnic et al. (2005)]. Many thanks to Berislav Lisnic for contributing the results and for assistance with the files.
#A new microarray dataset, "Expression in response to peroxisome induction and repression" ([http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000070290 Smith et al. 2002]), has been added to Expression Connection. This study compares the expression of each ''S. cerevisiae'' gene during metabolic shifts that either induce or repress peroxisome assembly and proliferation to identify genes involved in peroxisome biogenesis or function. We thank John Aitchison and Jennifer Smith for contributing their results and assisting us in loading the data. 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 Page or by clicking on the Expression Summary histogram. In addition, in order to provide a better representation of expression ratios over an increasing number of experiments the Expression Summary histogram has recently been modified for finer binning. Datasets in Expression Connection are also available for download from the SGD FTP site.
==Community News==
'''Programming position available at SGD'''
*We are looking for a motivated, experienced senior bioinformatician to help maintain and enhance the web pages and tools available at SGD. A detailed description of the position as well as instructions for applying can be found in the [http://stanfordcareers.stanford.edu/openings/display.cgi?Job_Req=010109&JFam=NIL&JOBCODE=5102 job posting] on Stanford's job website. Applications must be submitted via Stanford Jobs.
==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

*ESF-EMBO Symposium on Gene Transcription in Yeast*
:Sant Feliu de Guixols, Spain
:June 24 - June 29, 2006

*Yeast Chromosome Structure, Replication and Segregation (FASEB)*
:Indian Wells, CA
:June 24 - June 29, 2006

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

*24th Small Meeting on Yeast Transport and Energetics
:Prague, Czech Republic
:August 31 - September 3, 2006

*5th International Meeting on Yeast Apoptosis
:Kutna Hora, Czech Republic
:September 3 - September 7, 2006

*XXIIIrd International Conference on Yeast Genetics and Molecular Biology*
:Melbourne, Australia
:July 1 - July 6, 2007

 asterisks indicate attendance by SGD.* 
 '''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 \>
 <br>This is the May 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.<br \>
 ==Collaboation with BioGRID Makes 65,000+ Interactions Available at SGD==
 SGD has joined forces with [http://thebiogrid.org BioGRID] to provide a common dataset of budding yeast interactions. More than 65,000 genetic and physical interactions are now available from SGD. This dataset is described by Reguly et al. (2006), Comprehensive Curation and Analysis of Global Interaction Networks in ''Saccharomyces cerevisiae'', Journal of Biology, in press. SGD, BioGRID and the SGD Colony at Princeton are working together to maintain and update this complete dataset of yeast genetic and physical interactions. We thank Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark for their help in providing and loading the data.

SGD Quarterly Newsletter, Spring 2006 - Revision history

Kyla at 22:34, 19 December 2013

Kyla: Created page with "Category:Newsletter '''SGD Newsletter, May 2006''' '''About this newsletter:''' This is the May 2006 issue of the quarterly SGD newsletter..."

Kyla: Created page with "Category:Newsletter
'''SGD Newsletter, May 2006'''

'''About this newsletter:'''

This is the May 2006 issue of the quarterly SGD newsletter..."