SGD Quarterly Newsletter, Summer 2008

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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

Contents

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 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 Huttenhower C and Troyanskaya OG (2008) This method is described further in Myers et al., 2005, Myers et al., 2007, and Huttenhower et al., 2006. These data can be viewed in the computational GO annotation section (for example, see GO annotations for 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 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 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 BioGRID and a 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 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 Help Resources page. This pamphlet describes the content and usage of many resources available at SGD.

Add Protocols to the Wiki

A protocols and methods page is available on the 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
YDR341C YHR020W YLR003C YNL247W AIM10/YER087W ALA1/YOR335C
BFR2/YDR299W BMS1/YPL217C BUD21/YOR078W CDC60/YPL160W CTA1/YDR256C DBP8/YHR169W
DED81/YHR019C DIA4/YHR011W DIM1/YPL266W DIP2/YLR129W DPS1/YLL018C ECM16/YMR128W
EMG1/YLR186W ENP1/YBR247C ENP2/YGR145W FAB1/YFR019W FCF1/YDR339C FRS1/YLR060W
FRS2/YFL022C GCV3/YAL044C GLN4/YOR168W GRS1/YBR121C GRS2/YPR081C GUS1/YGL245W
HAS1/YMR290C HTS1/YPR033C ILS1/YBL076C IMP3/YHR148W IMP4/YNL075W INP51/YIL002C
INP52/YNL106C INP53/YOR109W INP54/YOL065C ISM1/YPL040C KRE33/YNL132W KRR1/YCL059C
KRS1/YDR037W LSB6/YJL100W MDJ1/YFL016C MES1/YGR264C MPP10/YJR002W MRD1/YPR112C
MSD1/YPL104W MSE1/YOL033W MSF1/YPR047W MSK1/YNL073W MSM1/YGR171C MSR1/YHR091C
MSS4/YDR208W MST1/YKL194C MSW1/YDR268W MSY1/YPL097W NAM2/YLR382C NAN1/YPL126W
NFU1/YKL040C NOC4/YPR144C NOP14/YDL148C NOP9/YJL010C PIK1/YNL267W PNO1/YOR145C
PWP2/YCR057C RCL1/YOL010W ROK1/YGL171W RRP12/YPL012W RRP5/YMR229C SAC1/YKL212W
SAS10/YDL153C SCL1/YGL011C SES1/YDR023W SLM5/YCR024C SLX9/YGR081C SNR17A/snR17a
SNU13/YEL026W SOD2/YHR008C SOF1/YLL011W STT4/YLR305C THS1/YIL078W TSR1/YDL060W
TYS1/YGR185C UTP10/YJL109C UTP11/YKL099C UTP13/YLR222C UTP14/YML093W UTP15/YMR093W
UTP18/YJL069C UTP20/YBL004W UTP21/YLR409C UTP22/YGR090W UTP23/YOR004W UTP30/YKR060W
UTP4/YDR324C UTP5/YDR398W UTP6/YDR449C UTP7/YER082C UTP8/YGR128C UTP9/YHR196W
VAS1/YGR094W VPS34/YLR240W WRS1/YOL097C YMR1/YJR110W 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 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 YDL038C, PRM7/YDL039C, BUD4/YJR092W, ASK1/YKL052C; the annotation of ORFs LSB3/YFR024C-A and ADH4/YGL256W on Chromosomes VI and VII were udpated; and a new LTR 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
Poster in PDF format


asterisks indicate attendance by SGD.*

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