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

This is the November 2006 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform ou..."

2013-12-19T19:57:27Z

Created page with "Category:Newsletter '''About this newsletter:''' This is the November 2006 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform ou..."

New page

[[Category:Newsletter]]
 '''About this newsletter:''' 
 This is the November 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. 

==New Paper on S288C Genome Annotation and Sequence Change==
''Yeast'' has recently published a paper authored by members of SGD. [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119159 Fisk, et al. ''Saccharomyces cerevisiae'' S288C genome annotation: a working hypothesis. Yeast 2006 Sep; 23(12):867-65] was written in celebration of the tenth anniversary of the completion of the ''S. cerevisiae'' genome sequence and discusses the ways in which the sequence and its annotation have changed in the decade since it was first published. The changes to the systematic sequence described in this publication can also be viewed via the Chromosome History pages.
==SGD Requests Feedback on Phenotype Information==
We are in the process of collecting and curating more comprehensive and referenced information about mutant phenotypes. As we develop new ways to display phenotype information and new ways to search it, we would like to ask for your feedback. Please send us your comments about:

*the type of phenotype information you'd like to see in SGD
*the types of searches you'd like to do
*ways in which phenotype information should be integrated with existing SGD tools (for instance, should it be a criterion for the Advanced Search? should the Quick Search look at the text of phenotypes?)

We appreciate your help in developing SGD!
==Updated Regulatory Regions in Genome Browser==
GBrowse has been updated to include an expanded "Regulatory regions & binding sites" section that can display data from multiple sources. To see this new display, you may need to toggle this track "All on" and then select the "Update Image" button. The first set of new data in this section was published by [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000081047 Tachibana, et al. (2005)] and we thank Chris Tachibana and Ted Young for working with SGD on incorporating their data. If your lab has data that would be appropriate to display in this section of GBrowse, please contact SGD curators.
==New Protein Pages and Proteome Browser==
We have enhanced the depth and accessibility of protein information at SGD through the redesign of the [http://www.yeastgenome.org/help/function-help/protein-information Protein Information] page, the Domains/Motifs page, and through the introduction of a Physico-chemical Properties page. These resources are available via the 'Protein' tab (pictured above) and 'Protein Info & Structure' pull-down menu on all Locus Summary pages. Inter-page navigability is also possible through the use of sub-tabs, located at the top of all Protein Information pages. In addition, a GBrowse-derived interactive Proteome Browser has also been introduced to enhance the visualization of protein sequence-based information. Thumbnail images available on all Protein Information and Domains/Motifs pages provide a point of entry to this interactive browser designed to consolidate the display of domains/motifs (InterPro), transmembrane regions (TMHMM), signal peptides (SignalP), and hydropathy plots. Please clear your browser's cache, located in either the preference or tools menu, if you are unable to view these changes.
==Sequence and Annotation Changes Made to the Systematic Sequence of ''S. cerevisiae''==
:::: '''List of Sequence Annotation Changes''' 
{| class="wikitable"
|-
| I || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=1#annot 2 ARS] elements || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=1#annot 3 ARS] elements
|-
| II || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000006478 LSR1] || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=2#annot 14 ARS] elements
|-
| III || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=3#annot 4 ARS] elements || None
|-
| IV || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=4#annot I ARS] element || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=4#annot 28 ARS] elements
|-
| V || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=5#annot 10 ARS] elements || None
|-
| VI || None || None
|-
| VII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003266 RPL26B/YGR034W] || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=7#annot 19 ARS] elements
|-
| VIII || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=4#annot I ARS] element || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=8#annot 8 ARS] elements
|-
| IX || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=4#annot I ARS] element || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=8#annot 8 ARS] elements
|-
| X || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003695 HSP150/YJL159W], [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=10#annot 7 ARS] elements || None
|-
| XI || None || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=11#annot 13 ARS] elements
|-
| XII || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000004304 MRPL15/YLR312W-A] || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=12#annot 16 ARS] elements
|-
| XIII || None || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000119075 SNR86/snR86], [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=13#annot 17 ARS] elements
|-
| XIV || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=1#annot 3 ARS] elements || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=14#annot 12 ARS] elements
|-
| XV || [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005737 MGM1/YOR211C], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005699 DCS2/YOR173W], [http://www.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000005486 MDH2/YOL126C], [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=4#annot I ARS] element || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=15#annot 14 ARS] elements
|-
| XVI || None || [http://www.yeastgenome.org/cgi-bin/chromosomeHistory.pl?chr=16#annot 19 ARS] elements
|-
| Mito || None || None
|}
==New ARS Data Added==
SGD has incorporated 171 new ARS elements with confirmed replication origin activity from Nieduszynski et al. 2006, greatly increasing the number of ''S. cerevisiae'' replication origins represented in SGD. See the 'Annotation Changes' section of the Chromosome History pages for more information. A link to OriDB, the DNA replication Origin DataBase, has also been added to SGD's External Links resource. Many thanks to Conrad Nieduszynski and Anne Donaldson at the University of Aberdeen for providing the data.
==New Cell Cycle Transcription Profiles Available==
A link to cell cycle transcription profiles has been added to the Functional Analysis pull-down menu on Locus Summary pages for all systematically named ORFs. These profiles were created based on the work of Pramila et al., 2006, who assayed alpha-factor synchronized cells for expression across the cell cycle using spotted cDNA arrays, and analyzed the results in conjunction with public domain data sets. In addition, an interactive resource entitled Periodic Genes of the Yeast ''Saccharomyces cerevisiae'' can be accessed in the Expression Data Resources section of the External Links page. Thanks to Linda Breeden and William Noble for generating the expression profile summary pages.
==BioGRID version 2.0.20 released (866 physical and genetic interactions added)==
The curated set of protein and genetic interactions described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000116320 Reguly et al., 2006] has been updated from the period November 1, 2005 to May 1, 2006, to include an additional 866 protein and genetic interactions; these data are available over the web and via bulk download through both [http://thebiogrid.org BioGRID] and SGD. This additional dataset brings the total number of literature curated interactions to 34,177. New interactions will be added in curation updates on a monthly basis, and these updated data will be available in both SGD and BioGRID. Please let us know of any missed or incorrectly reported interactions by sending an e-mail to gridadmin@mshri.on.ca.
==Search SGD Using Database Identifiers==
''S. cerevisiae'' genes or proteins can now be retrieved in SGD using UniProt IDs, E.C. numbers, GenBank/EMBL/DDBJ accession IDs, and NCBI Gene IDs. For example, the Locus Summary page for LEU2/YCL018W can be accessed by entering the E.C. number 1.1.1.85 or UniProt ID P04173 in the Quick Search. Accession IDs from NCBI and UniProt are updated weekly from the NCBI RefSeq and EMBL-EBI Genome Reviews databases. All data are available from the 'dbxref.tab' file in the chromosomal_feature/ directory on our FTP site.
==SGD Quick Reference Guide Available==
The 'SGD Quick Reference Guide' distributed at the 2006 YGMB meeting at Princeton is now available for download. This pamphlet describes the content and usage of many resources available at SGD. If you would like to receive hard copies of this pamphlet, please contact SGD (yeast-curator@yeastgenome.org) and we will be happy to mail them to you. This pamphlet can also be downloaded from SGD's Help Resources page.
==New Summary Paragraphs for 60 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 60 genes have been added to their respective Locus Summary pages.

:::::: '''Summary Paragraphs Added During the Last Quarter''' 
{| class="wikitable"
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADH6 ADH6/YMR318C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ADH7 ADH7/YCR105W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=APN1 APN1/YKL114C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=APN2 APN2/YBL019W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ASF1 ASF1/YJL115W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?dbid=S000001251 BAT1/YHR208W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=BAT2 BAT2/YJR148W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=CDC28 CDC28/YBR160W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COQ2#summaryparagraph COQ2/YNR041C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX1#summaryparagraph COX1/Q0045] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX12 COX12/YLR038C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX13 COX13/YGL191W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX2 COX2/Q0250] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX3 COX3/Q0275] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX4 COX4/YGL187C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX5A COX5A/YNL052W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX5B COX5B/YIL111W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX6 COX6/YHR051W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX7 COX7/YMR256C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX8 COX8/YLR395C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=COX9 COX9/YDL067C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=CSM4 CSM4/YPL200W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ENA1 ENA1/YDR040C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ENA2 ENA2/YDR039C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=ENA5 ENA5/YDR038C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FLP1 FLP1/R0010W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=FLX1 FLX1/YIL134W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL1 GAL1/YBR020W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL10 GAL10/YBR019C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL2 GAL2/YLR081W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL3 GAL3/YDR009W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL7 GAL7/YBR018C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=GAL80 GAL80/YML051W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=HEM1 HEM1/YDR232W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=HOG1 HOG1/YLR113W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=HPT1 HPT1/YDR399W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=KTI12 KTI12/YKL110C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LEU1 LEU1/YGL009C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LEU4 LEU4/YNL104C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LEU5 LEU5/YHR002W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=LEU9 LEU9/YOR108W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MET1 MET1/YKR069W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MSH1 MSH1/YHR120W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MSH2 MSH2/YOL090W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MSH3 MSH3/YCR092C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MSH6 MSH6/YDR097C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MYO1 MYO1/YHR023W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=MYO4 MYO4/YAL029C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=PFK1 PFK1/YGR240C] || PFK2/YMR205C || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAD18 RAD18/YCR066W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=RAF1 RAF1/R0030W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=REP1 REP1/R0020C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=REP2 REP2/R0040C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=SIN3 SIN3/YOL004W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=TOS3 TOS3/YGL179C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=WHI3 WHI3/YNL197C] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=WHI5 WHI5/YOR083W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=XPT1 XPT1/YJR133W] || [http://www.yeastgenome.org/cgi-bin/locus.pl?locus=YHC3 YHC3/YJL059W]
|}
==Community News==
*The 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 highlights a paper by Reguly et al., 2006 in which the authors made use of GO to evaluate interactions and networks.
*The IntAct team at EBI has been involved in developing guidelines for effectively reporting molecular interaction data. These guidelines are referred to as the Minimum Information required for reporting a Molecular Interaction experiment (MIMIx). A paper describing MIMIx is available on the Nature Biotechnology (NBT) website for community-review prior to publication. Please send your comments concerning this paper to NBT (biotech@natureny.com).
==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

*American Society of Cell Biology (ASCB)
:San Diego, CA
:December 9-13, 2006

*Experimental Biology Annual Meeting
:Washington, DC
:April 28 - May 2, 2007

*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]'''

SGD Quarterly Newsletter, Fall 2006 - Revision history

Kyla: Created page with "Category:Newsletter '''About this newsletter:''' This is the November 2006 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform ou..."

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

This is the November 2006 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform ou..."