SGD-Wiki - User contributions [en]

Methods

2011-05-10T15:15:23Z

SaulHonigberg:

*[http://labs.fhcrc.org/breeden/Methods/index.html Yeast Lab Protocols] from the Breeden Lab, Fred Hutchinson Cancer Research Center.

*[http://labs.fhcrc.org/gottschling/Yeast%20Protocols/index.html Yeast Lab Protocols] from the Gottschling Lab, Fred Hutchinson Cancer Research Center.

*[http://gasch.genetics.wisc.edu/protocols.html Yeast & Microarray Protocols] from the Gasch Lab, University of Wisconsin-Madison.

*[http://www.umanitoba.ca/faculties/medicine/biochem/gietz/Trafo.html The Definitive Yeast Transformation Homepage] from the University of Manitoba.

*[http://fangman-brewer.genetics.washington.edu/index.html DNA Replication Protocols] from the Fangman and Brewer Labs, University of Washington.

*[http://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html Interaction Trap at Work] information page from Erica Golemis's laboratory at the Fox Chase Cancer Center.

*[http://cmgm.stanford.edu/pbrown/mguide/index.html The MGuide. Version 2.0], a complete guide to microarraying for the molecular biologist, from the Brown Lab, Stanford University.

*[http://gasch.genetics.wisc.edu/protocols/Gasch_MethEnzym.pdf Guide to Yeast Microarray Experiments], by Audrey Gasch, from Guide to Yeast Genetics and Molecular and Cellular Biology, Methods in Enzymology (2002)

*The [http://depts.washington.edu/yeastrc/ NCRR Yeast Resource Center] at the University of Washington facilitates the study of yeast protein complexes by providing access to techniques such as mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction.

*Full text of the paper (Erdeniz et al. (1997) Genome Res. 7:1174-1183) describing [http://www.genome.org/cgi/content/full/7/12/1174 PCR-Based Allele Replacement]. Available to the public without password restriction and at no charge, through a special arrangement with Genome Research arranged by Rodney Rothstein (''see [[CommunityW303.html|detailed notes]] from RR and Stephan Bartsch for the W303 strain used in the study'').

*[http://genomics.princeton.edu/dunham/chemostat.html Chemostat Manual] from Maitreya Dunham's lab, Princeton University. See her [http://genomics.princeton.edu/dunham/protocols.shtml other protocols].

*[http://www.phys.ksu.edu/gene/chapters.html A Classroom Guide To Yeast Experiments] from The GENE project at Kansas State University based on [http://www.rushessay.com essay writing].

*[http://openwetware.org/wiki/The_mRNA_Decay_Resource:Protocols_and_Resources Protocols and Resources] from the RNA Decay Resource, a resource for the sharing of information, know-how, and wisdom among researchers who study mRNA decay.

*[[SGA]] SGA protocols and scoring software.

*[http://Vadlo.com Molecular Biology Protocols Search Engine] from Life in Research, LLC. Also life sciences databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases]

*[http://wiki.yeastgenome.org/index.php/Software Software tools] created by members of the scientific community.
*[http://sbs.umkc.edu/yeastcommunity Yeast Community Site] from Honigberg Lab, University of Missouri Kansas City.

External Links

2011-05-10T15:06:52Z

SaulHonigberg: /* General Yeast Resources */

=General Yeast Resources=
*[http://wiki.yeastgenome.org/index.php/General_Topics General Yeast Topics] describes the yeast model organisms: Saccharomyces cerevisiae (budding, bakers', and sometimes brewers'), Schizosaccharomyces pombe (fission), and Candida albicans. Includes information for non-specialists and teachers.

*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives] search the Yeast Biosci Newsgroup

=Nucleic Acid Data Resources=

*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank] sequence repository at the [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA

*[http://www.ebi.ac.uk/embl/index.html EMBL] sequence repository at the [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK

*[http://www.nig.ac.jp/index-e.html DDBJ] sequence repository at Mishima, Japan

*[http://www.genepalette.org/index.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences

*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae

*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.

*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms

*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of Saccharomyces cerevisiae] explore the promoter regions of all ORFs in the yeast genome. Note that this web site is not exhaustive, and some of the information is outdated.

*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in Saccharomyces spp.] search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, et al (2004) In Silico Biol 4(3):0034]]

*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz

*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts

*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz

=Genome and Protein Resources=

*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory] A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome

*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level. You can browse an [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.

*[http://genome.wustl.edu/tools/blast/ Genome Sequence Center: BLAST Server]at the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five Saccharomyces species: S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri.

*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])

*[http://www.incyte.com/control/tools/proteome Yeast Proteome Database (YPD)] yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.

*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte et al. (1999) Nature 402:83-86.]

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES - a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz et al. (2000) Nature 403:623-627.]

*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] a database of genetic and physical interactions. BioGRID, developed in Mike Tyers group, contains interaction data from many sources, including both small-scale and genome/proteome-wide studies, the [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.

*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] a powerful application for graphically representing physical and genetic biological interactions. It provides many features that are helpful in analysis of interaction data. Osprey is also coupled with the [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.

*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository] provides protein searching from multiple yeast databases and provides experimental data from mass spectrometry, yeast two-hybrid, fluorescence microscopy, protein structure prediction and protein complex predictions for S. cerevisiae proteins. Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.

*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.

*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].

*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between S. cerevisiae and S. pombe. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J] (Wellcome Trust Sanger Institute, Cambridge, UK).

*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several different Saccharomyces and Schizosaccharomyces strains

*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome

=Expression Data Resources=

*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D132 Monteiro et al.</a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).

*[http://sceptrans.org/ SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214 Kudlicki et al. (2007) Bioinformatics])

*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) [http://www.pnas.org/cgi/content/full/98/10/5631 Zhao LP, et al. (2001)] Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A 98(10):5631-6. [http://www.fhcrc.org/science/labs/breeden/spm/ View data], and (2) [http://www.yeasgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 Alter O, Brown PO, Botstein D (2000)] Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97(18):10101-6. [http://genome-www.stanford.edu/SVD/ View data].

*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast Saccharomyces cerevisiae] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila et al. (in press). This includes access to three new expression data sets generated using spotted cDNA arrays after sampling alpha factor synchronized cells across a time-course. Two of these data sets and three additional data sets from the public domain have been analyzed using a permutation based method published by [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) Bioinformatics 21:1164-71] to calculate a weighted average peak time base. This interactive resource allows users to sort and filter data, as well as access expression plots and heat maps.

*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in [http://nar.oxfordjournals.org/cgi/content/abstract/29/13/e63 Marc et al. (2001) Nucleic Acids Res 29(13):e63]

*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets

*[http://www.genmapp.org/ GenMAPP] a Visual Basic application that displays expression data on biochemical and cellular pathways as well as groups of genes.  MAPPFinder is a related tool that integrates GO annotations with GenMAPP to create a global expression profile (see [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003) Genome Biology 4:R7])

*[http://www.sagenet.org/index.htm Yeast SAGE] homepage for Serial Analysis of Gene Expression project at Johns Hopkins University

= Localization Data Resources=

*[http://images.yeastrc.org/ Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from S. cerevisiae, but also currently includes some S. pombe. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle et al (2010)] for more information.

*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] S. cerevisiae protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae

*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.

=Phenotype Data Resources=

*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page] A chemical genomics phenotype database to query for phenotypes of href="#deletions yeast deletion strains] grown in the presence of triterpene glycosides (TTG's) from the cactus Stenocereus gummosus (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.

*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] A collection of micrographs of budding yeast mutants. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000075221 Saito et al. (2004) Nucleic Acids Res 32:D319-22.]

*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.]

*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

=Additional Yeast Research Resources=

*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the Saccharomyces Genome Deletion project] are available via [http://www.atcc.org ATCC] ([http://www.atcc.org/catalog/all/allIndex.cfm online catalog] available), [http://www.openbiosystems.com/ Open Biosystems], and [http://mp.invitrogen.com/ Invitrogen] (Research Genetics). The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.

*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]

*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ Sanger Institute] and [http://www.nottingham.ac.uk/genetics/people/louis/index.php?from=genContact&ID=205&S=Yeast%20Genomic%20Resources Prof. Ed Louis' group] at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.

*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of S. cerevisiae systems biology by facilitating cooperation between experimental scientists and theoreticians, generating quantitative data, and developing new resources. Download YSBN's [http:www.yeastgenome.org/community/ysbn.pdf brochure] for more information and contacts.

*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org:8080/pgvec1?f=c&cmd=showfile&file=colinfo Search] for a plasmid or [http://www.addgene.org/pgvec1?f=d&cmd=showfile&file=submit deposit] your plasmid to the repository.

=Other Resources=
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.

*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page

*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan

*[http://restools.sdsc.edu/ Molecular Biology] resources from CMS. An impressive set of hyperlinks with a great presentation on all aspects of molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.

*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs

*[http://www.microbes.info/ Microbes.info] The Microbiology Information Portal. This site contains resources, news, and information about many different aspects of microbiology. Its [http://www.microbes.info/resources/General_Microbiology/ General Microbiology] section contains links to various databases, culture collections, genetic analysis sites, and method sites.

*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group

*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources

*[http://www.nature.com/Scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

=Nucleic Acids Research Database Issues=
Articles about genomic and biological databases.
Go to NAR Database Issue for: 
[http://nar.oxfordjournals.org/content/38/suppl_1 2010]|
[http://nar.oxfordjournals.org/content/37/suppl_1 2009] |
[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl 2008] |
[http://nar.oxfordjournals.org/content/vol35/suppl_1/ 2007] |
[http://nar.oxfordjournals.org/content/vol34/suppl_1/ 2006] |
[http://nar.oxfordjournals.org/content/vol33/suppl_1/ 2005] |
[http://nar.oxfordjournals.org/content/vol32/suppl_1/ 2004] |
[http://nar.oxfordjournals.org/content/vol31/issue1/ 2003] |
[http://nar.oxfordjournals.org/content/vol30/issue1/ 2002] |
[http://nar.oxfordjournals.org/content/vol29/issue1/ 2001] |
[http://nar.oxfordjournals.org/content/vol28/issue1/ 2000] |
[http://nar.oxfordjournals.org/content/vol27/issue1/ 1999] |
[http://nar.oxfordjournals.org/content/vol26/issue1/ 1998] |

 
View SGD's article for: 
[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D577 2008] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D468 2007] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D442 2006] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D374 2005]|
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D311 2004] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/31/1/216 2003] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/30/1/69 2002] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/29/1/80 2001] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/28/1/77 2000] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/27/1/74 1999] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/26/1/73 1998]

External Links

2011-05-10T05:27:40Z

SaulHonigberg: /* General Yeast Resources */

=General Yeast Resources=
*[http://wiki.yeastgenome.org/index.php/General_Topics General Yeast Topics] describes the yeast model organisms: Saccharomyces cerevisiae (budding, bakers', and sometimes brewers'), Schizosaccharomyces pombe (fission), and Candida albicans. Includes information for non-specialists and teachers.

*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives] search the Yeast Biosci Newsgroup

*[http://sbs.umkc.edu/yeastcommunity Yeast Community Site] provided by University of Kansas City, Missouri Biology Lab.

=Nucleic Acid Data Resources=

*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank] sequence repository at the [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA

*[http://www.ebi.ac.uk/embl/index.html EMBL] sequence repository at the [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK

*[http://www.nig.ac.jp/index-e.html DDBJ] sequence repository at Mishima, Japan

*[http://www.genepalette.org/index.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences

*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae

*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.

*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms

*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of Saccharomyces cerevisiae] explore the promoter regions of all ORFs in the yeast genome. Note that this web site is not exhaustive, and some of the information is outdated.

*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in Saccharomyces spp.] search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, et al (2004) In Silico Biol 4(3):0034]]

*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz

*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts

*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz

=Genome and Protein Resources=

*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory] A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome

*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level. You can browse an [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.

*[http://genome.wustl.edu/tools/blast/ Genome Sequence Center: BLAST Server]at the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five Saccharomyces species: S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri.

*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])

*[http://www.incyte.com/control/tools/proteome Yeast Proteome Database (YPD)] yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.

*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte et al. (1999) Nature 402:83-86.]

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES - a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz et al. (2000) Nature 403:623-627.]

*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] a database of genetic and physical interactions. BioGRID, developed in Mike Tyers group, contains interaction data from many sources, including both small-scale and genome/proteome-wide studies, the [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.

*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] a powerful application for graphically representing physical and genetic biological interactions. It provides many features that are helpful in analysis of interaction data. Osprey is also coupled with the [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.

*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository] provides protein searching from multiple yeast databases and provides experimental data from mass spectrometry, yeast two-hybrid, fluorescence microscopy, protein structure prediction and protein complex predictions for S. cerevisiae proteins. Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.

*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.

*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].

*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between S. cerevisiae and S. pombe. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J] (Wellcome Trust Sanger Institute, Cambridge, UK).

*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several different Saccharomyces and Schizosaccharomyces strains

*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome

=Expression Data Resources=

*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D132 Monteiro et al.</a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).

*[http://sceptrans.org/ SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214 Kudlicki et al. (2007) Bioinformatics])

*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) [http://www.pnas.org/cgi/content/full/98/10/5631 Zhao LP, et al. (2001)] Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A 98(10):5631-6. [http://www.fhcrc.org/science/labs/breeden/spm/ View data], and (2) [http://www.yeasgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 Alter O, Brown PO, Botstein D (2000)] Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97(18):10101-6. [http://genome-www.stanford.edu/SVD/ View data].

*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast Saccharomyces cerevisiae] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila et al. (in press). This includes access to three new expression data sets generated using spotted cDNA arrays after sampling alpha factor synchronized cells across a time-course. Two of these data sets and three additional data sets from the public domain have been analyzed using a permutation based method published by [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) Bioinformatics 21:1164-71] to calculate a weighted average peak time base. This interactive resource allows users to sort and filter data, as well as access expression plots and heat maps.

*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in [http://nar.oxfordjournals.org/cgi/content/abstract/29/13/e63 Marc et al. (2001) Nucleic Acids Res 29(13):e63]

*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets

*[http://www.genmapp.org/ GenMAPP] a Visual Basic application that displays expression data on biochemical and cellular pathways as well as groups of genes.  MAPPFinder is a related tool that integrates GO annotations with GenMAPP to create a global expression profile (see [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003) Genome Biology 4:R7])

*[http://www.sagenet.org/index.htm Yeast SAGE] homepage for Serial Analysis of Gene Expression project at Johns Hopkins University

= Localization Data Resources=

*[http://images.yeastrc.org/ Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from S. cerevisiae, but also currently includes some S. pombe. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle et al (2010)] for more information.

*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] S. cerevisiae protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae

*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.

=Phenotype Data Resources=

*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page] A chemical genomics phenotype database to query for phenotypes of href="#deletions yeast deletion strains] grown in the presence of triterpene glycosides (TTG's) from the cactus Stenocereus gummosus (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.

*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] A collection of micrographs of budding yeast mutants. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000075221 Saito et al. (2004) Nucleic Acids Res 32:D319-22.]

*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.]

*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

=Additional Yeast Research Resources=

*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the Saccharomyces Genome Deletion project] are available via [http://www.atcc.org ATCC] ([http://www.atcc.org/catalog/all/allIndex.cfm online catalog] available), [http://www.openbiosystems.com/ Open Biosystems], and [http://mp.invitrogen.com/ Invitrogen] (Research Genetics). The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.

*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]

*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ Sanger Institute] and [http://www.nottingham.ac.uk/genetics/people/louis/index.php?from=genContact&ID=205&S=Yeast%20Genomic%20Resources Prof. Ed Louis' group] at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.

*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of S. cerevisiae systems biology by facilitating cooperation between experimental scientists and theoreticians, generating quantitative data, and developing new resources. Download YSBN's [http:www.yeastgenome.org/community/ysbn.pdf brochure] for more information and contacts.

*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org:8080/pgvec1?f=c&cmd=showfile&file=colinfo Search] for a plasmid or [http://www.addgene.org/pgvec1?f=d&cmd=showfile&file=submit deposit] your plasmid to the repository.

=Other Resources=
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.

*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page

*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan

*[http://restools.sdsc.edu/ Molecular Biology] resources from CMS. An impressive set of hyperlinks with a great presentation on all aspects of molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.

*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs

*[http://www.microbes.info/ Microbes.info] The Microbiology Information Portal. This site contains resources, news, and information about many different aspects of microbiology. Its [http://www.microbes.info/resources/General_Microbiology/ General Microbiology] section contains links to various databases, culture collections, genetic analysis sites, and method sites.

*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group

*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources

*[http://www.nature.com/Scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

=Nucleic Acids Research Database Issues=
Articles about genomic and biological databases.
Go to NAR Database Issue for: 
[http://nar.oxfordjournals.org/content/38/suppl_1 2010]|
[http://nar.oxfordjournals.org/content/37/suppl_1 2009] |
[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl 2008] |
[http://nar.oxfordjournals.org/content/vol35/suppl_1/ 2007] |
[http://nar.oxfordjournals.org/content/vol34/suppl_1/ 2006] |
[http://nar.oxfordjournals.org/content/vol33/suppl_1/ 2005] |
[http://nar.oxfordjournals.org/content/vol32/suppl_1/ 2004] |
[http://nar.oxfordjournals.org/content/vol31/issue1/ 2003] |
[http://nar.oxfordjournals.org/content/vol30/issue1/ 2002] |
[http://nar.oxfordjournals.org/content/vol29/issue1/ 2001] |
[http://nar.oxfordjournals.org/content/vol28/issue1/ 2000] |
[http://nar.oxfordjournals.org/content/vol27/issue1/ 1999] |
[http://nar.oxfordjournals.org/content/vol26/issue1/ 1998] |

 
View SGD's article for: 
[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D577 2008] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D468 2007] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D442 2006] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D374 2005]|
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D311 2004] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/31/1/216 2003] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/30/1/69 2002] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/29/1/80 2001] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/28/1/77 2000] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/27/1/74 1999] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/26/1/73 1998]

External Links

2011-05-10T05:19:09Z

SaulHonigberg: /* General Yeast Resources */

=General Yeast Resources=
*[http://wiki.yeastgenome.org/index.php/General_Topics General Yeast Topics] describes the yeast model organisms: Saccharomyces cerevisiae (budding, bakers', and sometimes brewers'), Schizosaccharomyces pombe (fission), and Candida albicans. Includes information for non-specialists and teachers.

*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives] search the Yeast Biosci Newsgroup

*[http://sbs.umkc.edu/yeastcommunity/] provided by University of Kansas City, Missouri Biology Lab.

=Nucleic Acid Data Resources=

*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank] sequence repository at the [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA

*[http://www.ebi.ac.uk/embl/index.html EMBL] sequence repository at the [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK

*[http://www.nig.ac.jp/index-e.html DDBJ] sequence repository at Mishima, Japan

*[http://www.genepalette.org/index.html GenePalette] software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences

*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae

*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool] explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.

*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms

*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of Saccharomyces cerevisiae] explore the promoter regions of all ORFs in the yeast genome. Note that this web site is not exhaustive, and some of the information is outdated.

*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in Saccharomyces spp.] search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, et al (2004) In Silico Biol 4(3):0034]]

*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz

*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs] yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts

*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz

=Genome and Protein Resources=

*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory] A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome

*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins] This website provides structural assignments to protein sequences at the superfamily level. You can browse an [http://supfam.org/SUPERFAMILY/cgi-bin/gen_list.cgi?genome=sc overview] of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11697912&dopt=Abstract Gough et al.] for more information.

*[http://genome.wustl.edu/tools/blast/ Genome Sequence Center: BLAST Server]at the Washington University GSC in St. Louis. BLAST searches may be performed against genomic sequences from five Saccharomyces species: S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri.

*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS] yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])

*[http://www.incyte.com/control/tools/proteome Yeast Proteome Database (YPD)] yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.

*[http://www.doe-mbi.ucla.edu/Services/GPofYPF/index.html Genome-Wide Protein Function Prediction] Links between functionally related yeast proteins are used to predict functions for about two thirds of all predicted yeast proteins in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000044838 Marcotte et al. (1999) Nature 402:83-86.]

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES - a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map] The Fields lab's systematic Two-Hybrid project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz et al. (2000) Nature 403:623-627.]

*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)] a database of genetic and physical interactions. BioGRID, developed in Mike Tyers group, contains interaction data from many sources, including both small-scale and genome/proteome-wide studies, the [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.

*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System] a powerful application for graphically representing physical and genetic biological interactions. It provides many features that are helpful in analysis of interaction data. Osprey is also coupled with the [http://www.thebiogrid.org/ General Repository of Interaction Datasets (BioGRID)] and as a result brings a large dataset of interactions to your fingertips.

*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository] provides protein searching from multiple yeast databases and provides experimental data from mass spectrometry, yeast two-hybrid, fluorescence microscopy, protein structure prediction and protein complex predictions for S. cerevisiae proteins. Please see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?pubmed=15608220 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82] for more information.

*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)] a database of mass spectrometry based proteomics information, populated by the general proteomics community.

*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from S. cerevisiae, S. castellii, C. glabrata, A. gossypii, K. lactis, K. waltii, and S. kluyveri. This tool was developed by Kevin Byrne and Ken Wolfe (Trinity College, Dublin, Ireland), as described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000113653 Byrne and Wolfe].

*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe, and Saccharomyces cerevisiae). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between S. cerevisiae and S. pombe. This tool was developed by [http://www.sanger.ac.uk/PostGenomics/S_pombe/ Penkett CJ, Morris JA, Wood V, and Bahler J] (Wellcome Trust Sanger Institute, Cambridge, UK).

*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several different Saccharomyces and Schizosaccharomyces strains

*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome

=Expression Data Resources=

*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)] A curated database of regulatory associations between transcription factors and their target genes, and information on transcription factor binding sites (see [http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D132 Monteiro et al.</a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).

*[http://sceptrans.org/ SCEPTRANS] A website for visualizing and studying periodic transcription in yeast (see [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000122214 Kudlicki et al. (2007) Bioinformatics])

*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects] Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) [http://www.pnas.org/cgi/content/full/98/10/5631 Zhao LP, et al. (2001)] Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc Natl Acad Sci U S A 98(10):5631-6. [http://www.fhcrc.org/science/labs/breeden/spm/ View data], and (2) [http://www.yeasgenome.org/cgi-bin/reference/reference.pl?dbid=S000060075 Alter O, Brown PO, Botstein D (2000)] Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci U S A 97(18):10101-6. [http://genome-www.stanford.edu/SVD/ View data].

*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast Saccharomyces cerevisiae] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila et al. (in press). This includes access to three new expression data sets generated using spotted cDNA arrays after sampling alpha factor synchronized cells across a time-course. Two of these data sets and three additional data sets from the public domain have been analyzed using a permutation based method published by [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15513999&dopt=Abstract de Lichtenberg et al. (2005) Bioinformatics 21:1164-71] to calculate a weighted average peak time base. This interactive resource allows users to sort and filter data, as well as access expression plots and heat maps.

*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer] a database containing most of the published yeast microarray expression datasets as described in [http://nar.oxfordjournals.org/cgi/content/abstract/29/13/e63 Marc et al. (2001) Nucleic Acids Res 29(13):e63]

*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets

*[http://www.genmapp.org/ GenMAPP] a Visual Basic application that displays expression data on biochemical and cellular pathways as well as groups of genes.  MAPPFinder is a related tool that integrates GO annotations with GenMAPP to create a global expression profile (see [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003) Genome Biology 4:R7])

*[http://www.sagenet.org/index.htm Yeast SAGE] homepage for Serial Analysis of Gene Expression project at Johns Hopkins University

= Localization Data Resources=

*[http://images.yeastrc.org/ Yeast Resource Center Public Image Repository (YRC PIR)] Very large repository of images and metadata from fluorescence microscopy experiments, including localization, colocalization and FRET experiments. Mostly contains data from S. cerevisiae, but also currently includes some S. pombe. Submission of data is welcome and encouraged. Please see [http://www.ncbi.nlm.nih.gov/pubmed/20482811 Riffle et al (2010)] for more information.

*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] S. cerevisiae protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit] images.

*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression] Yeast transposon tagging data from the [http://ygac.med.yale.edu Yale Genome Analysis Center.]

*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library] A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae

*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] S. cerevisiae protein localization data from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.

=Phenotype Data Resources=

*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page] A chemical genomics phenotype database to query for phenotypes of href="#deletions yeast deletion strains] grown in the presence of triterpene glycosides (TTG's) from the cactus Stenocereus gummosus (common name agria). Pre-publication access provided by Scott Erdman at Syracuse University.

*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)] A collection of micrographs of budding yeast mutants. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000075221 Saito et al. (2004) Nucleic Acids Res 32:D319-22.]

*[http://prophecy.lundberg.gu.se/ PROPHECY] A database that provides quantitative information regarding growth rate, growth efficiency, and adaptation time for haploid deletion strains. For more information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000119344 Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.]

*[http://genomics.senescence.info/genes/models.html GenAge] GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

=Additional Yeast Research Resources=

*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the Saccharomyces Genome Deletion project] are available via [http://www.atcc.org ATCC] ([http://www.atcc.org/catalog/all/allIndex.cfm online catalog] available), [http://www.openbiosystems.com/ Open Biosystems], and [http://mp.invitrogen.com/ Invitrogen] (Research Genetics). The [http://www-sequence.stanford.edu/group/yeast_deletion_project/gb/ykocp.html Community Posting Page] provided by the [http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Saccharomyces Genome Deletion Project] enables users of the mutant collection to share information about the collection. [http://web.uni-frankfurt.de/fb15/mikro/euroscarf/ EUROSCARF] makes deletion strains available from the EUROFAN projects.

*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center] Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]

*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)] A colloboration between the [http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ Sanger Institute] and [http://www.nottingham.ac.uk/genetics/people/louis/index.php?from=genContact&ID=205&S=Yeast%20Genomic%20Resources Prof. Ed Louis' group] at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.

*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of S. cerevisiae systems biology by facilitating cooperation between experimental scientists and theoreticians, generating quantitative data, and developing new resources. Download YSBN's [http:www.yeastgenome.org/community/ysbn.pdf brochure] for more information and contacts.

*[http://www.addgene.org Addgene] Repository and distributor of plasmid constructs described in published literature. [http://www.addgene.org:8080/pgvec1?f=c&cmd=showfile&file=colinfo Search] for a plasmid or [http://www.addgene.org/pgvec1?f=d&cmd=showfile&file=submit deposit] your plasmid to the repository.

=Other Resources=
*[http://www.openhelix.com/sgd SGD Tutorial] Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.

*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page

*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan

*[http://restools.sdsc.edu/ Molecular Biology] resources from CMS. An impressive set of hyperlinks with a great presentation on all aspects of molecular biology, biotechnology, molecular evolution, biochemistry, and biomolecular modeling.

*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs

*[http://www.microbes.info/ Microbes.info] The Microbiology Information Portal. This site contains resources, news, and information about many different aspects of microbiology. Its [http://www.microbes.info/resources/General_Microbiology/ General Microbiology] section contains links to various databases, culture collections, genetic analysis sites, and method sites.

*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group

*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources

*[http://www.nature.com/Scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

=Nucleic Acids Research Database Issues=
Articles about genomic and biological databases.
Go to NAR Database Issue for: 
[http://nar.oxfordjournals.org/content/38/suppl_1 2010]|
[http://nar.oxfordjournals.org/content/37/suppl_1 2009] |
[http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl 2008] |
[http://nar.oxfordjournals.org/content/vol35/suppl_1/ 2007] |
[http://nar.oxfordjournals.org/content/vol34/suppl_1/ 2006] |
[http://nar.oxfordjournals.org/content/vol33/suppl_1/ 2005] |
[http://nar.oxfordjournals.org/content/vol32/suppl_1/ 2004] |
[http://nar.oxfordjournals.org/content/vol31/issue1/ 2003] |
[http://nar.oxfordjournals.org/content/vol30/issue1/ 2002] |
[http://nar.oxfordjournals.org/content/vol29/issue1/ 2001] |
[http://nar.oxfordjournals.org/content/vol28/issue1/ 2000] |
[http://nar.oxfordjournals.org/content/vol27/issue1/ 1999] |
[http://nar.oxfordjournals.org/content/vol26/issue1/ 1998] |

 
View SGD's article for: 
[http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D577 2008] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D468 2007] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D442 2006] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D374 2005]|
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/32/suppl_1/D311 2004] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/31/1/216 2003] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/30/1/69 2002] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/29/1/80 2001] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/28/1/77 2000] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/27/1/74 1999] |
[http://www.yeastgenome.org/cgi-bin/redirect.pl?source=ExternalContens&url=http://nar.oxfordjournals.org/cgi/content/full/26/1/73 1998]

External Links

2011-05-10T05:16:34Z

SaulHonigberg: /* Other Resources */[http://sbs.umkc.edu/yeastcommunity/] provided by the University of Kansas City Missouri Biology lab