Kyla at 22:34, 19 December 2013

2013-12-19T22:34:26Z

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

'''About this newsletter:'''

This is the July 2006 issue of the quarterly SGD newslett..."

2013-12-19T20:01:01Z

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

New page

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

==Visit SGD at the Yeast Genetics and Molecular Biology Meeting - Win a T-shirt or Cap==
Members of the SGD staff will be present at the 2006 Yeast Genetics and Molecular Biology Meeting at Princeton University from July 25 - 30, 2006. In addition to presenting posters about data and resources available at SGD, we will be soliciting your feedback on how data should be organized. Stop by our demo table and you could win a limited edition SGD T-shirt or cap.
==Search for a Strain Background and more in 44,000+ Yeast-Related Full Text Articles==
The SGD full-text literature search (powered by [http://www.textpresso.org Textpresso]) has been expanded, and now includes 44,000+ yeast-related full-text journal articles. The full-text literature search can be accessed via the Full-text search link on the home page, from a link on the SGD Search Options contents page, and from the Literature pulldown menu on the right side of all Locus Summary Pages, where the search form is prefilled with the ORF or gene name.
==View Updates to the Systematic Sequence on New Chromosome History Pages==
New Chromosome History pages have been implemented to view sequence and annotation changes made to the systematic sequence of ''S. cerevisiae''. These pages display the complete sequence and annotation history of each chromosome since the initial release of the systematic reference sequence on 1996-07-31. Chromosome Histories can be accessed through the Chromosome History Search via the Sequencing Tables link at the bottom left of the home page under Download Data.
==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 16 features. Altered or new features are listed in the What's New in SGD for 2006. Details regarding these changes can be found in the Chromosome History (see above) of each chromosome 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 || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006463 CEN1] || None
|-
| II || None || None
|-
| III || None || None
|-
| IV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006466 CEN4] || None
|-
| V || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000000764 UTR4/YEL038W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006467 CEN5] || None
|-
| VI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001896 CEN6] || None
|-
| VII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006468 CEN7] || None
|-
| VIII || None || None
|-
| IX || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006470 CEN9] || None
|-
| X || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003763 YJR003C] || None
|-
| XI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001690 EMC3/YKL207W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001651 KKQ8/YKL168C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001744 CAF4/YKR036C] || None
|-
| XII || None || None
|-
| XIII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000004663 SEN15/YMR059W] || None
|-
| XIV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005254 ZIM17/YNL310C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005146 SPS19/YNL202W] || None
|-
| XV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005723 MCA1/YOR197W] || None
|-
| XVI || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006477 CEN16] || None
|-
| Mito || None || None
|}
==Transcription Factor Data Remapped to Updated Sequence==
The transcription factor binding sites published by [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000081155 Harbison et al. (2004)] have been remapped to the current ''S. cerevisiae'' genome sequence. These data can be viewed in GBrowse and in the "Regulatory Role" section on the Locus Summary Pages (see [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=sum1 SUM1]). In addition, the regulatory map data from [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000114654 Maclsaac et al. (2006)] are available from the FTP site. Thanks to Kenzie MacIsaac for providing information to remap the binding sites and new data to SGD.
==New Summary Paragraphs for 115 Genes and Chromosomal Features==
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 115 genes and chromosomal 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?dbid=S000002622 AHA1/YDR214W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004301 CDC25/YLR310C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006093 COX10/YPL172C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000000943 COX15/YER141W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000005225 HCH1/YNL281W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004798 HSC82/YMR186W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000003949 HSP104/YLL026W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006161 HSP82/YPL240C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000002214 MBP1/YDL056W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000005767 MET7/YOR241W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000001369 PFK26/YIL107C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000005496#summaryParagraph PFK27/YOL136C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000003131#summaryParagraph RAD54/YGL163C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004045 SPT8/YLR055C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000000537 STE50/YCL032W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000002953 YRF1-1/YDR545W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000000992 YRF1-2/YER190W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000003528 YRF1-3/YGR296W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004458 YRF1-4/YLR466W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000004459 YRF1-5/YLR467W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000005283 YRF1-6/YNL339C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006204 YRF1-7/YPL283C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077372 ARS101/ARS109] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028457 ARS1020]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007553 ARS1021] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028458 ARS1022] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028459 ARS1023] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028460 ARS1024] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028461 ARS1025] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114488 ARS110]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114848 ARS1208] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077373 ARS1411] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077374 ARS1412] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077375 ARS1413] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077376 ARS1414] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007554 ARS1501]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007643 ARS1502] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114843 ARS1516] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114517 ARS209] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028476 ARS300] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028477 ARS301] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028478#summaryParagraph ARS302]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028479 ARS303] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028481 ARS304] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028482 ARS305] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028483 ARS306] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028484 ARS307] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028485 ARS308]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028486 ARS309] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028487 ARS310] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028488 ARS313] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028489 ARS314] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028490 ARS315] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028491 ARS316]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028492 ARS317] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028493 ARS318] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028494 ARS319] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028480 ARS320] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114787 ARS404] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000029652 ARS1/ARS416]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114834 ARS422] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077377 ARS502] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077378 ARS503] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077379 ARS504] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077380 ARS507] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077381 ARS508]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077382 ARS510] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077383 ARS511] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077384 ARS512] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077385 ARS513] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077386 ARS514] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077387 ARS515]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077388 ARS516] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077389 ARS517] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077390 ARS518] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077391 ARS519] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077392 ARS520] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077393 ARS521]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077394 ARS522] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000077395 ARS523] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000029653 ARS600] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007633 ARS601] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007634 ARS602] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007635 ARS603]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007645 ARS603.5] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007636 ARS604] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007637 ARS605] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007638 ARS606] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007639 ARS607] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007640 ARS608]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007641 ARS609] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007642 ARS701] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114845 ARS706] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000114849 ARS805] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000029042 ARS2/ARS808] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000007644 ARS901/ARS913]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028438 ARS1001] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028439 ARS1002] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028440 ARS1003] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028441 ARS1004] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028442 ARS1005] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028443 ARS1006]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028444 ARS1007] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028445 ARS1008] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028446 ARS1009] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028447 ARS1010] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028448 ARS1011] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028449 ARS1012]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028450 ARS1013] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028451 ARS1014] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028452 ARS1015] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028453 ARS1016] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028454 ARS1017] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028455 ARS1018]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000028456 ARS1019] || || || || ||
|}

==New Datasets Added==
#SGD has added data to its FTP site (systematic_results directory) from [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=16510898 Kastenmayer JP et al. (2006)], a study that describes the phenotypes of gene-deletion mutants of 247 small open reading frames (sORFs) in ''S. cerevisiae''. These deletion strains are available as supplemental sets from [http://www.thermoscientificbio.com/openbiosystems/?redirect=true Open Biosystems].
#The regulatory map data from [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000114654 MacIsaac, et al. (2006)] are available from the FTP site. Thanks to Kenzie MacIsaac for providing the new data to SGD.
==Community News==
*The [http://www.geneontology.org Gene Ontology Consortium] began publishing a newsletter to highlight significant improvements and changes to the ontologies, annotations, and software that are developed by members of the GO Consortium. This newsletter will be sent to those subscribed to the GO Friends mailing list on a quarterly basis. The current newsletter includes a basic tutorial on [http://amigo.geneontology.org/cgi-bin/amigo/go.cgi AmiGO].
*A new resource to search periodic genes of the yeast Saccharomyces cerevisiae based on a combined analysis of five cell cycle microarray datasets (Pramila, et al., in press) has been added to the Expression Data Resources on the External Links page.
==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

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

*Interactome Networks *
:Wellcome Trust Genome Campus, Hinxton, UK
:August 30 - September 3, 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

*Yeast Genome 10th anniversary *
:Brussels, Belgium
:September 7 - September 8, 2006

*Genome Informatics *
:Wellcome Trust Genome Campus, Hinxton, UK
:September 13 - September 17, 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 July 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 \>

SGD Quarterly Newsletter, Summer 2006 - Revision history

Kyla at 22:34, 19 December 2013

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

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

'''About this newsletter:'''

This is the July 2006 issue of the quarterly SGD newslett..."