Kyla at 22:32, 19 December 2013

2013-12-19T22:32:27Z

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

This is the July 2008 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our us..."

2013-12-19T20:12:36Z

Created page with "Category:Newsletter '''About this newsletter:''' This is the July 2008 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 2008 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] 

==Expanded Phenotype Data and New Curation System==
SGD is now releasing our improved and expanded mutant phenotype pages. Over the past year, we re-curated existing mutant phenotypes and added more phenotype data, both using a new controlled-vocabulary system. The implementation of this system greatly increases the amount of detailed information that can be captured for each phenotype, and facilitates searching and comparison of mutant phenotypes. A brief version of the phenotype is displayed on the Locus Summary page for each gene, and the complete information is accessible via the 'Phenotype' tab at the top of the page (for example, see [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL197C WHI3]). Each phenotype annotation contains a term representing the entity or process that is observed (e.g., sporulation efficiency, carbon source utilization, cell size) and a qualifier that describes the effect on that entity or process in the mutant (e.g., decreased, increased, abnormal). Additional fields display information such as strain background, allele name, conditions under which the phenotype is observed, or the identity of relevant chemicals. SGD now contains more than 25,000 phenotype annotations, nearly double the previous number, and we will continue to build upon this annotation with the aim of providing comprehensive phenotype information. All of the information is searchable and may also be downloaded in bulk using SGD's Batch Download tool or FTP site.
==Functional Predictions Available as GO Annotations==
SGD has incorporated computational GO annotations from the functional predictions based on the analysis of multiple high-throughput datasets published in [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=18586732 Huttenhower C and Troyanskaya OG (2008)] This method is described further in [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=16420673 Myers et al., 2005], [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=17599939 Myers et al., 2007], and [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=17005538 Huttenhower et al., 2006]. These data can be viewed in the computational GO annotation section (for example, see GO annotations for [http://db.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?dbid=S000002315 CMR1/YDL156W]). Thanks to Curtis Huttenhower and Olga Troyanskaya for working with SGD on incorporating these data.

SGD has incorporated computational GO annotations from a method published in [http://db.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=18613951 Tian et al., Genome Biology 2008] that combines guilt-by-profiling and guilt-by-association analysis to infer gene function. These data can be viewed in the computational GO annotation section (for example, see GO annotations for [http://db.yeastgenome.org/cgi-bin/GO/goAnnotation.pl?dbid=S000000637 YCR041W]). Links to gene pages at the YeastFunc viewer are available on the GO Annotation details page in the 'Assigned By' column and in the 'Functional Analysis' pull-down on the right hand side of the Locus Summary pages. Thanks to Weidong Tian, John Beaver, and Fritz Roth for working with SGD on incorporating these data and links.
==Improvements to the SGD Search==
The SGD Quick Search has been expanded to retrieve information from 14 major categories including: names, descriptions, functional information, phenotype data, colleagues, authors, and external IDs. Results are now organized under topic headings that group similar types of information. This basic search is accessible from the top of most SGD pages, as well as from the Search Options page.
==Improved Display, Sorting and Filtering of Interaction Data==
The Interactions page has been updated to allow physical and genetic interactions to be sorted and filtered based on an experimental method, reference, or phenotype. This table also includes notes about the interaction as well as the annotation type to facilitate the identification of high-throughput datasets. SGD now includes 121,580 curated physical and genetic interactions from the BioGRID version 2.0.42 release. New interactions are added on a monthly basis. These data are available over the web and via bulk download through both [http://thebiogrid.org BioGRID] and a [http://wiki.yeastgenome.org/index.php/Specification_for_New_Interactions_and_Phenotype_FTP_files new FTP file] at SGD.
==Download ''S. cerevisiae'' Biochemical Pathways poster==
Due to popular demand, the Biochemical Pathways poster on display at the 2008 YGMB meeting in Toronto is now available for download from the [http://pathway.yeastgenome.org Biochemical Pathways page]. The poster can be printed for easy viewing and display as a wall chart.
==SGD Quick Reference Guide Available==
The 'SGD Quick Reference Guide' distributed at the 2008 YGMB meeting in Toronto is now available for download from SGD's [http://www.yeastgenome.org/help Help Resources page]. This pamphlet describes the content and usage of many resources available at SGD.
==Add Protocols to the Wiki==
A [http://wiki.yeastgenome.org/index.php/Methods protocols and methods page] is available on the [http://wiki.yeastgenome.org/index.php/Main_Page Community Wiki] to allow researchers to post useful protocols. This page is linked from the 'Protocols and Methods' link listed in the navigation menu. These pages can be edited by clicking the 'edit' tab at the top of the page.
==Summary Paragraphs Progress, 108 new since May 2008==
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 2008 - July 2008), new summary paragraphs for the following 105 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.fpl?locus=YDR341C YDR341C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR020W YHR020W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR003C YLR003C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL247W YNL247W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YER087W AIM10/YER087W] ||[http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOR335C ALA1/YOR335C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR299W BFR2/YDR299W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL217C BMS1/YPL217C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOR078W BUD21/YOR078W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL160W CDC60/YPL160W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR256C CTA1/YDR256C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR169W DBP8/YHR169W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR019C DED81/YHR019C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR011W DIA4/YHR011W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL266W DIM1/YPL266W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR129W# DIP2/YLR129W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLL018C DPS1/YLL018C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YMR128W ECM16/YMR128W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR186W EMG1/YLR186W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YBR247C ENP1/YBR247C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR145W ENP2/YGR145W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YFR019W FAB1/YFR019W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR339C FCF1/YDR339C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR060W FRS1/YLR060W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YFL022C FRS2/YFL022C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YAL044C GCV3/YAL044C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOR168W GLN4/YOR168W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YBR121C GRS1/YBR121C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPR081C GRS2/YPR081C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGL245W GUS1/YGL245W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YMR290C HAS1/YMR290C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPR033C HTS1/YPR033C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YBL076C ILS1/YBL076C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR148W IMP3/YHR148W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL075W IMP4/YNL075W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YIL002C INP51/YIL002C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL106C INP52/YNL106C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOR109W INP53/YOR109W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOL065C INP54/YOL065C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL040C ISM1/YPL040C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL132W KRE33/YNL132W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YCL059C KRR1/YCL059C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR037W KRS1/YDR037W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YJL100W LSB6/YJL100W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YFL016C MDJ1/YFL016C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR264C MES1/YGR264C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YJR002W MPP10/YJR002W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPR112C MRD1/YPR112C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL104W MSD1/YPL104W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOL033W MSE1/YOL033W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPR047W MSF1/YPR047W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL073W MSK1/YNL073W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR171C MSM1/YGR171C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR091C MSR1/YHR091C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR208W MSS4/YDR208W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YKL194C MST1/YKL194C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR268W MSW1/YDR268W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL097W MSY1/YPL097W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR382C NAM2/YLR382C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL126W NAN1/YPL126W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YKL040C NFU1/YKL040C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPR144C NOC4/YPR144C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDL148C NOP14/YDL148C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YJL010C NOP9/YJL010C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL267W PIK1/YNL267W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOR145C PNO1/YOR145C]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YCR057C PWP2/YCR057C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOL010W RCL1/YOL010W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGL171W ROK1/YGL171W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YPL012W RRP12/YPL012W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YMR229C RRP5/YMR229C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YKL212W SAC1/YKL212W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDL153C SAS10/YDL153C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGL011C SCL1/YGL011C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR023W SES1/YDR023W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YCR024C SLM5/YCR024C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR081C SLX9/YGR081C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=snR17a SNR17A/snR17a]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YEL026W SNU13/YEL026W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR008C SOD2/YHR008C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLL011W SOF1/YLL011W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR305C STT4/YLR305C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YIL078W THS1/YIL078W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDL060W TSR1/YDL060W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR185C TYS1/YGR185C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YJL109C UTP10/YJL109C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YKL099C UTP11/YKL099C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR222C UTP13/YLR222C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YML093W UTP14/YML093W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YMR093W UTP15/YMR093W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YJL069C UTP18/YJL069C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YBL004W UTP20/YBL004W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR409C UTP21/YLR409C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR090W UTP22/YGR090W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOR004W UTP23/YOR004W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YKR060W UTP30/YKR060W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR324C UTP4/YDR324C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR398W UTP5/YDR398W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YDR449C UTP6/YDR449C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YER082C UTP7/YER082C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR128C UTP8/YGR128C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YHR196W UTP9/YHR196W]
|-
| [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YGR094W VAS1/YGR094W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YLR240W VPS34/YLR240W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YOL097C WRS1/YOL097C] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YJR110W YMR1/YJR110W] || [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL325C FIG4/YNL325C]
|}

==Six sequence/annotation changes made to the systematic sequence of ''S. cerevisiae''==
As new data become available, SGD curators update the systematic genomic sequence, its gene models, and their annotation. Information regarding sequence and annotation changes can be found via the [http://db.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 2008 - July 2008), the sequences of Chromosomes IV, X, and XI were updated, affecting ORFs [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002196 YDL038C], [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002197 PRM7/YDL039C], [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003852 BUD4/YJR092W], [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000001535 ASK1/YKL052C]; the annotation of ORFs [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000002968 LSB3/YFR024C-A] and [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000003225 ADH4/YGL256W] on Chromosomes VI and VII were udpated; and a new LTR [http://db.yeastgenome.org/cgi-bin/locusHistory.pl?dbid=S000126593 YCLWdelta15] was annotated on Chromosome III.
==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

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

*12th International Congress on Yeasts
:Kyiv Aviation University, Kyiv (Kiev), Ukraine
:August 11 - August 15, 2008

*Small Meeting on Yeast Transport and Energetics
:Bom Jesus, Braga, Portugal
:September 6-9, 2008

*EMBO Workshop on Evolutionary and Environmental Genomics of Yeasts
:EMBL Heidelberg, Germany
:October 1 - 5, 2008

*XXIV International Conference on Yeast Genetics and Molecular Biology
:University of Manchester
:Manchester, United Kingdom
:July 19 - 24, 2009
:[http://www.yeastgenome.org/community/meetings/yeast09/Yeast2009-Announcement.pdf Poster in PDF format]

 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 2008 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 \>
 ==Expanded Phenotype Data and New Curation System==
 SGD is now releasing our improved and expanded mutant phenotype pages. Over the past year, we re-curated existing mutant phenotypes and added more phenotype data, both using a new controlled-vocabulary system. The implementation of this system greatly increases the amount of detailed information that can be captured for each phenotype, and facilitates searching and comparison of mutant phenotypes. A brief version of the phenotype is displayed on the Locus Summary page for each gene, and the complete information is accessible via the 'Phenotype' tab at the top of the page (for example, see [http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=YNL197C WHI3]). Each phenotype annotation contains a term representing the entity or process that is observed (e.g., sporulation efficiency, carbon source utilization, cell size) and a qualifier that describes the effect on that entity or process in the mutant (e.g., decreased, increased, abnormal). Additional fields display information such as strain background, allele name, conditions under which the phenotype is observed, or the identity of relevant chemicals. SGD now contains more than 25,000 phenotype annotations, nearly double the previous number, and we will continue to build upon this annotation with the aim of providing comprehensive phenotype information. All of the information is searchable and may also be downloaded in bulk using SGD's Batch Download tool or FTP site.

SGD Quarterly Newsletter, Summer 2008 - Revision history

Kyla at 22:32, 19 December 2013

Kyla: Created page with "Category:Newsletter '''About this newsletter:''' This is the July 2008 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 2008 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our us..."