Kyla at 22:33, 19 December 2013

2013-12-19T22:33:19Z

Kyla: Created page with "Category:Newsletter
'''About this newsletter:'''

This is the July 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our us..."

2013-12-19T20:09:42Z

Created page with "Category:Newsletter '''About this newsletter:''' This is the July 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our us..."

New page

[[Category:Newsletter]]
 '''About this newsletter:''' 
 This is the July 2007 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 can also subscribe to SGD's RSS feed to receive updates on SGD news - http://www.yeastgenome.org/feed 

 Details of these items can be viewed at the [http://www.yeastgenome.org/blog SGD Blog] 

==Transcription Data in Genome Browser==
Transcription start sites reported in [http://http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15905473 Zhang Z and Dietrich FS (2005) Nucleic Acid Res 33:2838] and cDNA clones reported in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=17101987 Miura F et al. (2006) Proc Natl Acad Sci USA 103:17846] can be viewed in the Genome Browser. To view these data, select the "cDNA transcripts" and "Transcription start sites" tracks and press the "Update Image" button. If you do not see those tracks, select the red "Reset" button. The data are available from SGD's FTP site. Thanks to Takashi Ito, Fumihito Miura, Shinichi Morishita, and Fred Dietrich for working with SGD on incorporating these data.
==How many Uncharacterized yeast genes?==
Huges & Pena-Castillo's paper [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=17435240 Why are there still over 1000 uncharacterized yeast genes?] is available as a PDF from SGD's FTP site. We thank [http://www.genetics.org Genetics] for generously providing the freely distributable PDF of this paper.
In addition, the list of Uncharacterized ORFs analyzed in this recent publication is available from the same location of the FTP site. SGD staff have reviewed the status of the 126 named genes mentioned in the paper and have upgraded over half of them to Verified status based on recent publications. A current list of Uncharacterized ORFs can be retrieved via SGD's Genome Snapshot or Advanced Search.
SGD classifies ORFs as Verified, Uncharacterized, and Dubious according to the degree of certainty that each ORF encodes a functional protein. SGD considers these classifications a working hypothesis, and the designations change based on published experimental results.
==Links to Protein, Strain and Expression Websites Added==
*Links to [http://moment.utmb.edu/cgi-bin/sceptrans.cgi SCEPTRANS], a resource to view and analyze periodic transcription profiles from multiple publications, has been added to SGD. SCEPTRANS can be accessed by selecting the 'Cell cycle and metabolic oscillation' option in the Functional Analysis pull-down menu on Locus Summary Pages for all systematically named ORFs. See [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214 Kudlicki A et al. (2007) Bioinformatics] for more information. Thanks to Andrzej Kudlicki for generating the summary pages for each ORF.
*Links to structural annotations for predicted domains at the [http://www.yeastrc.org/pdr/pages/front.jsp Yeast Resource Center Public Data Repository] have been added for 4640 proteins. These links are available via the "Protein Info" tab at the top of the Locus Summary page and through the "Protein Info & Structure" pull-down menu located on the right side of the Locus Summary page. See [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000121973 Malmstrom et al. PLoS Biol. 2007] for more information. Thanks to Michael Riffle and Trisha Davis for setting up the links.
*Links to the [http://yeast.lab.nig.ac.jp/nig/index_en.html Yeast Genetics Resource Center], a strain and plasmid resource in Japan, have been added for all ORFs. These links are available via the "Phenotypes" tab at the top of the Locus Summary page for each ORF. Thanks to Chikashi Shimoda and Yukiko Yamazaki for setting up the links.
==Improvements to SGD software==
Over the past six months, SGD staff have worked to improve the software that generates SGD web pages. As a consequence, many pages, including the Locus Summary and Literature Guide pages, have the same information and layout, but have been restyled for a more uniform, updated look. These changes will facilitate future expansion at SGD. Please do not hesitate to contact us with any bug reports or comments.
==New Summary Paragraphs==
Summary Paragraphs summarize published biological information for a gene/feature, 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 (May - July 2007), new summary paragraphs for the following 159 features have been added to their respective Locus Summary pages.

:::::: '''List of Summary Paragraphs Added During the Last Quarter''' 
{| class="wikitable"
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YPR021C AGC1/YPR021C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YIL033C BCY1/YIL033C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDL220C CDC13/YDL220C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR054C CDC34/YDR054C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBR109C CMD1/YBR109C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=Q0105 COB/Q0105] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBL045C COR1/YBL045C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJL005W CYR1/YJL005W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOR065W CYT1/YOR065W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOR005C DNL4/YOR005C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR233C EST1/YLR233C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR318W EST2/YLR318W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YIL009C-A EST3/YIL009C-A] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR342W FKS1/YLR342W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR306W FKS3/YMR306W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBL016W FUS3/YBL016W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR307W GAS1/YMR307W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR343W GAS2/YLR343W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR215W GAS3/YMR215W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOL132W GAS4/YOL132W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOL030W GAS5/YOL030W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YHR005C GPA1/YHR005C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGR032W GSC2/YGR032W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YPL127C HHO1/YPL127C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBR072W HSP26/YBR072W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR171W HSP42/YDR171W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=hta1 HTA1/YDR225W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=hta2 HTA2/YBL003C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGR040W KSS1/YGR040W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGL090W LIF1/YGL090W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR035C MLH2/YLR035C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YPL164C MLH3/YPL164C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOR269W PAC1/YOR269W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR044C PDC1/YLR044C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR134W PDC5/YLR134W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGR087C PDC6/YGR087C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YKL197C PEX1/YKL197C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJL210W PEX2/YJL210W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR329C PEX3/YDR329C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR244W PEX5/YDR244W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YNL329C PEX6/YNL329C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR142C PEX7/YDR142C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR265W PEX10/YDR265W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR026C PEX12/YMR026C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR191W PEX13/YLR191W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGL153W PEX14/YGL153W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YNL214W PEX17/YNL214W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YHR160C PEX18/YHR160C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDL065C PEX19/YDL065C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGR239C PEX21/YGR239C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YNL082W PMS1/YNL082W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBR088C POL30/YBR088C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR297W PRC1/YMR297W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YPR191W QCR2/YPR191W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YFR033C QCR6/YFR033C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YDR529C QCR7/YDR529C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJL166W QCR8/YJL166W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGR183C QCR9/YGR183C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YHR001W-A QCR10/YHR001W-A] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJR035W RAD26/YJR035W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YEL024W RIP1/YEL024W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YOL121C RPS19A/YOL121C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YNL302C RPS19B/YNL302C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YER120W SCS2/YER120W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBL091C-A SCS22/YBL091C-A]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YIL113W SDP1/YIL113W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YHL022C SPO11/YHL022C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YLR452C SST2/YLR452C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SUC1 SUC1/SUC1] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YIL162W SUC2/YIL162W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SUC3 SUC3/SUC3] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SUC4 SUC4/SUC4] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SUC5 SUC5/SUC5] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SUC7 SUC7/SUC7] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TLC1 TLC1/TLC1]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YJL164C TPK1/YJL164C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YPL203W TPK2/YPL203W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YKL166C TPK3/YKL166C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YGR019W UGA1/YGR019W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YBR006W UGA2/YBR006W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YML007W YAP1/YML007W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR284W YKU70/YMR284W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YMR106C YKU80/YMR106C] || 76 snoRNA genes ||
|}

==Annotation Changes Made to the Systematic Sequence of ''S. cerevisiae''==
As new data become available, SGD curators update the systematic sequence and its annotation. Information regarding sequence and annotation changes can be found via the [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl Summary of Chromosome Sequence and Annotation Updates] and in the "Locus History" pages of affected features. Files on the SGD FTP site are updated weekly. During the last quarter (May - July 2007), annotation changes were made affecting 10 RNA genes and new introns were annotated within 9 protein-coding features. 1 new feature was added.
{| class="wikitable"
|-
! Chromosome !! Annotation Changes !! New Features
|-
| I || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR18 snR18], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=HRA1 HRA1] || None
|-
| II || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YBR215W HPC2/YBR215W] || None
|-
| III || None || None
|-
| IV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YDL115C IWR1/YDL115C] || None
|-
| V || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YEL003W GIM4/YEL003W] || None
|-
| VI || None || None
|-
| VII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR46 snR46] || None
|-
| VIII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YHR076W PTC7/YHR076W] || None
|-
| IX || None || None
|-
| X || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR3 snR3] || None
|-
| XI || None || None
|-
| XII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR30 snR30], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR34 snR34] || None
|-
| XIII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR78 snR78], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YML036W CGI121/YML036W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YMR242C RPL20A/YMR242C] || None
|-
| XIV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YNL004W HRB1/YNL004W] || None
|-
| XV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR35 snR35], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR36 snR36], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YOR312C RPL20B/YOR312C] || None
|-
| XVI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=snR70 snR70], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YPR153W YPR153W] || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?locus=YPR010C-A YPR010C-A]
|}
==Upcoming Conferences and Meetings==
Information on registration and abstract deadlines for the following conferences is available at:
http://wiki.yeastgenome.org/index.php/Meetings#Upcoming_Conferences_.26_Courses

*Yeast Cell Biology*
:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
:August 15 - 19, 2007
:Abstract Deadline: May 23, 2007

*ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution
:Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain
:October 20 - 25, 2007
:Abstract Deadline: August 1, 2007

*Genome Informatics*
:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
:November 1 - 5, 2007
:Abstract Deadline: August 1, 2007

*Genetic Analysis: Model Organisms to Human Biology Meeting
:Town and Country Resort & Conference Center, San Diego, CA
:January 5 - 9, 2008
:Abstract Deadline: November 14, 2007

*Cellular & Molecular Fungal Biology
:Holderness School, Plymouth, NH
:June 29 - July 4, 2008
:Application Deadline: June 8, 2008

*Yeast Genetics and Molecular Biology Meeting*
:University of Toronto, Toronto, Ontario, Canada
:July 22-27, 2008
:Abstract Deadline: TBA
:For more information contact: mahoney@genetics-gsa.org

*Plant & Fungal Cytoskeleton
:Il Ciocco, Lucca (Barga), Italy
:August 3 - 8, 2008
:Application Deadline: July 13, 2008

 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 2: / Line 2: @@
 <br>'''About this newsletter:'''<br \>
 <br>This is the July 2007 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 can also subscribe to SGD's RSS feed to receive updates on SGD news - http://www.yeastgenome.org/feed<br \>
 ==Transcription Data in Genome Browser==
 Transcription start sites reported in [http://http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15905473 Zhang Z and Dietrich FS (2005) Nucleic Acid Res 33:2838] and cDNA clones reported in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=17101987 Miura F et al. (2006) Proc Natl Acad Sci USA 103:17846] can be viewed in the Genome Browser. To view these data, select the "cDNA transcripts" and "Transcription start sites" tracks and press the "Update Image" button. If you do not see those tracks, select the red "Reset" button. The data are available from SGD's FTP site. Thanks to Takashi Ito, Fumihito Miura, Shinichi Morishita, and Fred Dietrich for working with SGD on incorporating these data.

SGD Quarterly Newsletter, Summer 2007 - Revision history

Kyla at 22:33, 19 December 2013

Kyla: Created page with "Category:Newsletter '''About this newsletter:''' This is the July 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our us..."

Kyla: Created page with "Category:Newsletter
'''About this newsletter:'''

This is the July 2007 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our us..."