Difference between revisions of "External Links"

From SGD-Wiki
Jump to: navigation, search
(Created page with '=General Yeast Resources= *[http://wiki.yeastgenome.org/index.php/General_Topics General Yeast Topics] describes the yeast model organisms: <i>Saccharomyces cerevisiae </i>(buddi…')
 
Line 1: Line 1:
 
=General Yeast Resources=
 
=General Yeast Resources=
*[http://wiki.yeastgenome.org/index.php/General_Topics General Yeast Topics]
+
*[http://wiki.yeastgenome.org/index.php/General_Topics General Yeast Topics] describes the yeast model organisms: <i>Saccharomyces cerevisiae </i>(budding, bakers', and sometimes brewers'), <i>Schizosaccharomyces pombe </i>(fission), and <i>Candida albicans</i>. Includes information for non-specialists and teachers.<BR><BR>
describes the yeast model organisms: <i>Saccharomyces cerevisiae </i>(budding, bakers', and sometimes brewers'), <i>Schizosaccharomyces pombe </i>(fission), and <i>Candida albicans</i>. Includes information for non-specialists and teachers.<BR><BR>
 
  
*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives]
+
*[http://www.bio.net/hypermail/yeast/ BioSci Yeast Archives] search the Yeast Biosci Newsgroup
search the Yeast Biosci Newsgroup
 
  
 
=Nucleic Acid Data Resources=
 
=Nucleic Acid Data Resources=
  
*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank]
+
*[http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html GenBank] sequence repository at the  [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA<BR><BR>
sequence repository at the  [http://www.ncbi.nlm.nih.gov/ NCBI], Bethesda, Maryland, USA<BR><BR>
 
  
*[http://www.ebi.ac.uk/embl/index.html EMBL]
+
*[http://www.ebi.ac.uk/embl/index.html EMBL] sequence repository at the  [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK<BR><BR>
sequence repository at the  [http://www.ebi.ac.uk/ EBI], Hinxton Hall, Cambridge, UK<BR><BR>
 
  
*[http://www.nig.ac.jp/index-e.html DDBJ]
+
*[http://www.nig.ac.jp/index-e.html DDBJ] sequence repository at Mishima, Japan<BR><BR>
sequence repository at Mishima, Japan<BR><BR>
 
  
*[http://www.genepalette.org/index.html GenePalette]
+
*[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<BR><BR>
software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences<BR><BR>
 
  
*[http://www.oridb.org OriDB]
+
*[http://www.oridb.org OriDB] catalog of confirmed and predicted DNA replication origin sites, currently limited to <i>S. cerevisiae</i><br><br>
catalog of confirmed and predicted DNA replication origin sites, currently limited to <i>S. cerevisiae</i><br><br>
 
  
*[http://seq.cbrc.jp/~wataru/PROSPECT/ PROSPECT: Promoter Inspection Tool]
+
*[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.<BR><BR>
explore promoter regions by searching for genes or a sequence.  Also contains a list of yeast transcription factor binding sites.<BR><BR>
 
  
*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools]
+
*[http://rsat.ulb.ac.be/rsat/ Regulatory Sequence Analysis Tools] search for regulatory signals in the non-coding sequences of <I>S. cerevisiae, S. pombe,</I> and other organisms<BR><BR>
search for regulatory signals in the non-coding sequences of <I>S. cerevisiae, S. pombe,</I> and other organisms<BR><BR>
 
  
*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of <i>Saccharomyces cerevisiae</i>]
+
*[http://rulai.cshl.edu/SCPD/ SCPD: The Promoter Database of <i>Saccharomyces cerevisiae</i>] 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.<BR><BR>
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.<BR><BR>
 
  
*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in <i>Saccharomyces</i> spp.]
+
*[http://www2.imtech.res.in/anand/sacch_prom_pat.html Search for conserved patterns in <i>Saccharomyces</i> spp.] search tool for identification and analysis of conserved patterns in <i>Saccharomyces</i> promoters.  Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, <i>et al</i> (2004) <i>In Silico Biol</i> 4(3):0034]]<BR><BR>
search tool for identification and analysis of conserved patterns in <i>Saccharomyces</i> promoters.  Formore information, please refer to [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000079651 Kohli DK, <i>et al</i> (2004) <i>In Silico Biol</i> 4(3):0034]]<BR><BR>
 
  
<!-- this link goes to YGOB which is reiterated below
+
*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns] yeast intron data from the Ares Lab, U.C. Santa Cruz<BR><BR>
  
*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Duplications]
+
*[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<BR><BR>
gene duplication data from Ken Wolfe, Trinity -->
 
<!-- College, Dublin<BR><BR>
 
-->
 
*[http://www.cse.ucsc.edu/research/compbio/yeast_introns.html Yeast Introns]
 
yeast intron data from the Ares Lab, U.C. Santa Cruz<BR><BR>
 
  
*[http://people.biochem.umass.edu/fournierlab/snornadb/main.php Yeast snoRNAs]
+
*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs] yeast tRNA information from Todd Lowe, UC-Santa Cruz<br><br>
yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts<BR><BR>
 
 
 
*[http://lowelab.cse.ucsc.edu/GtRNAdb/Sacc_cere/ Yeast tRNAs]
 
yeast tRNA information from Todd Lowe, UC-Santa Cruz<br><br>
 
 
 
<!-- link is dead
 
 
 
*[http://biochimica.unipr.it/yeast/tRNA.html Yeast tRNAs]
 
yeast tRNA information from Riccardo Percudani, Universita' di Parma, Italy. Results are described in  *[http://www.idealibrary.com/links/doi/10.1006/jmbi.1997.0942/full Percudani <i>et al.</i> (1997) JMB 268</b>(2):322-330]<BR><BR>
 
 
 
-->
 
 
 
<!-- link is dead
 
 
 
*[http://www.leicester.ac.uk/genetics/ejl12/research/telostruc/EndsData.html Yeast Telomeres]
 
yeast telomere data from  *[http://www.leicester.ac.uk/genetics/ejl12/index.html Ed Louis' Lab], Univ. of Leicester, U. K.</BR>
 
 
 
-->
 
  
 
=Genome and Protein Resources=
 
=Genome and Protein Resources=
  
*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory]
+
*[http://www.yeastgenome.org/community/nature_genome_dir_pdf/ Yeast Genome Directory] A collection of papers describing the sequencing of each chromosome of the <i>S. cerevisiae</i> genome<BR><BR>
A collection of papers describing the sequencing of each chromosome of the <i>S. cerevisiae</i> genome<BR><BR>
 
  
*[http://supfam.org/SUPERFAMILY/index.html Structural assignments of proteins]
+
*[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 <i>S. cerevisiae</i>; 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.<BR><BR>
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 <i>S. cerevisiae</i>; 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.<BR><BR>
 
  
 
*[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 <i>Saccharomyces</i> species: <i>S. mikatae, S. kudriavzevii, S. bayanus, S. castellii,</i> and <i>S. kluyveri</i>.<br><br>
 
*[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 <i>Saccharomyces</i> species: <i>S. mikatae, S. kudriavzevii, S. bayanus, S. castellii,</i> and <i>S. kluyveri</i>.<br><br>
  
*[http://mips.gsf.de/proj/yeast/CYGD/db/index.html Yeast Project at MIPS]
+
*[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])<BR><BR>
yeast information from the Munich Information Center for Protein Sequences ([http://mips.gsf.de/ MIPS])<BR><BR>
 
 
 
*[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.<BR><BR>
 
<!--*[http://www.embl-heidelberg.de/predictprotein/predictprotein.html PredictProtein]
 
program for protein structure prediction, from
 
the Protein Design Group
 
at [http://www.ebi.ac.uk/embl/index.html EMBL]<BR><BR> -->
 
*[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 <i>et al.</i> (1999) <i>Nature</i> 402:83-86.]<BR><BR>
 
 
 
<!--
 
  
*[http://www.bind.ca/ BIND: the Biomolecular Interaction Network Database]  
+
*[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.<BR><BR>
collected information about protein-protein
 
interactions, complexes, and pathways. See the [http://www.blueprint.org/bind/bind_news.html BIND news] page for the latest developments.<BR><BR>  
 
  
-->
+
*[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 <i>et al.</i> (1999) <i>Nature</i> 402:83-86.]<BR><BR>
*[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.]<BR><BR>
 
  
*[http://depts.washington.edu/~sfields/yp_interactions/index.html Yeast Protein Linkage Map]
+
*[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.]<BR><BR>
The Fields lab's systematic Two-Hybrid
 
project. Results are described in [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000043128 Uetz <i>et al.</i> (2000) <i>Nature</i> 403:623-627.]
 
<!--  no longer available at CuraGen (emailed webmaster to check,  Jan. 2008)
 
A supporting  *[http://portal.curagen.com web site] is available to the public.
 
-->
 
  
 +
*[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 <i>et al.</i> (2000) <i>Nature</i> 403:623-627.]
  
*[http://www.thebiogrid.org/ General Repository for Interaction Datasets (BioGRID)]
+
*[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
a database of genetic and physical interactions.   
+
genome/proteome-wide studies, the [http://mips.gsf.de/proj/yeast/CYGD/db/index.html MIPS] database, and BIND.<BR><BR>
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.<BR><BR>
 
  
*[http://biodata.mshri.on.ca/osprey/servlet/Index Osprey: A Network Visualization System]
+
*[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.<BR><BR>
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.<BR><BR>
 
  
*[http://www.yeastrc.org/pdr/ Yeast Resource Center Public Data Repository]
+
*[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 <i>S. cerevisiae</i> 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.<BR><BR>
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 <i>S. cerevisiae</i>
 
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.<BR><BR>
 
  
*[http://gpmdb.thegpm.org/gpmdb_help.html The Global Proteome Machine Database (GPMDB)]
+
*[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.<BR><BR>
a database of mass spectrometry based proteomics information, populated by the general proteomics community.<BR><BR>
 
  
*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser]
+
*[http://wolfe.gen.tcd.ie/ygob/ Yeast Gene Order Browser] a tool used to visualize the syntenic context of any gene from
a tool used to visualize the syntenic context of any gene from
+
<i>S. cerevisiae</i>, <i>S. castellii</i>, <i>C. glabrata</i>, <i>A. gossypii</i>, <i>K. lactis</i>, <i>K. waltii</i>, and
<i>S. cerevisiae</i>, <i>S. castellii</i>, <i>C. glabrata</i>,
+
<i>S. kluyveri</i>. 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].<br><br>
<i>A. gossypii</i>, <i>K. lactis</i>, <i>K. waltii</i>, and
 
<i>S. kluyveri</i>. 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].<br><br>
 
  
*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY]  
+
*[http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/index.shtml YOGY:eukarYotic OrtholoGY] a tool to view orthologous proteins from eukaryotic orgranisms (<i>Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana,
a tool to view orthologous proteins from eukaryotic orgranisms
+
Drosophila melanogaster, Caenorhabditis elegans, Plasmodium falciparum, Schizosaccharomyces pombe</i>, and <i>Saccharomyces
(<i>Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana,
+
cerevisiae</i>). This tool provides information from KOGs, Inparanoid, Homologene, OrthoMCL and manually curated orthologs between <i>S. cerevisiae </i> and <i>S. pombe</i>. 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).<br><br>
Drosophila melanogaster, Caenorhabditis elegans, Plasmodium
 
falciparum, Schizosaccharomyces pombe</i>, and <i>Saccharomyces
 
cerevisiae</i>). This tool provides information from KOGs, Inparanoid,
 
Homologene, OrthoMCL and manually curated orthologs between <i>S. cerevisiae </i> and <i>S. pombe</i>. 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).<br><br>
 
  
*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast]  
+
*[http://www.binofo.com/en/bioinformatics/iproto/ iProto Yeast] an iPhone application containing proteome information for several
an iPhone application containing proteome information for several
 
 
different <i>Saccharomyces</i> and <i>Schizosaccharomyces</i> strains<br><br>
 
different <i>Saccharomyces</i> and <i>Schizosaccharomyces</i> strains<br><br>
  
*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions]  
+
*[http://refnucl.atlas.bx.psu.edu/ Yeast Nucleosome Positions] a compiled and systematic reference map of nucleosome positions across the <i>S. cerevisiae</i> genome<BR><BR>
a compiled and systematic reference map of nucleosome positions across the <i>S. cerevisiae</i> genome<BR><BR>
 
  
  
 
=Expression Data Resources=
 
=Expression Data Resources=
  
*[http://www.yeastract.com/ YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking)]
+
*[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 <i>et al.</i></a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136). <br><br>
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 <i>et al.</i></a], (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136). <br><br>
 
  
*[http://sceptrans.org/ SCEPTRANS]
+
*[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]) <br><br>
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]) <br><br>
 
  
*[http://genome-www.stanford.edu/cellcycle/ Yeast Cell Cycle Analysis Projects]
+
*[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  href="/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman <i>et al.</i> (1998) <i>Mol Cell Biol</i> 9:</b>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].<BR><BR>
Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies  href="/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman <i>et al.</i> (1998) <i>Mol Cell Biol</i> 9:</b>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].<BR><BR>
 
  
*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast <i>Saccharomyces cerevisiae</i>]
+
*[http://www.fhcrc.org/science/labs/breeden/cellcycle/ Periodic Genes of the Yeast <i>Saccharomyces cerevisiae</i>] A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila <i>et al.</i> (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) <i>Bioinformatics</i> 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.<BR><BR>
A combined analysis of five cell cycle microarray data sets, has been published in G&D by Pramila <i>et al.</i> (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) <i>Bioinformatics</i> 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.<BR><BR>
 
  
*[http://www.transcriptome.ens.fr/ymgv/ Yeast Microarray Global Viewer]
+
*[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<i> et al.</i> (2001) <i>Nucleic Acids Res</i> 29(13):e63] <BR><BR>
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<i> et al.</i> (2001) <i>Nucleic Acids Res</i> 29(13):e63] <BR><BR>
 
  
*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays ]
+
*[http://www-stat.stanford.edu/~tibs/PAM/ PAM: Prediction Analysis for Microarrays] a software tool for interpretation of microarray expression datasets <BR><BR>
a software tool for interpretation of microarray expression datasets <BR><BR>
 
  
*[http://www.genmapp.org/ GenMAPP]
+
*[http://www.genmapp.org/ GenMAPP] a Visual Basic application that displays expression data on biochemical and cellular pathways as well as groups of genes. <!-- (link is dead) Existing pathways can be  [http://www.genmapp.org/download.asp downloaded] for
a Visual Basic application that displays expression data on biochemical
+
use with the GenMAPP application or new pathways can be created and submitted.  --> 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) <i>Genome Biology</i> 4:R7])<br><br>
and cellular pathways as well as groups of genes. <!-- (link is dead) Existing pathways
 
can be  [http://www.genmapp.org/download.asp downloaded] for
 
use with the GenMAPP application or new pathways can be created and
 
submitted.  --> <b>MAPPFinder</b> 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) <i>Genome Biology</i> 4:R7])<br><br>
 
  
*[http://www.sagenet.org/index.htm Yeast SAGE]
+
*[http://www.sagenet.org/index.htm Yeast SAGE] homepage for Serial Analysis of Gene Expression project at Johns Hopkins University<BR><BR>
homepage for Serial Analysis of Gene Expression project at Johns Hopkins University<BR><BR>
 
  
  
 
= Localization Data Resources=
 
= Localization Data Resources=
  
*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)]  
+
*[http://ypl.uni-graz.at/pages/home.html YeastProtein Localization database (YPL.db)] <i>S. cerevisiae</i> protein localization data from University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit]
<i>S. cerevisiae</i> protein localization data from
 
University Graz. Users may also [http://wwwoas.kfunigraz.ac.at:8010/pls/al12/submit.logon submit]
 
 
images.<BR><BR>
 
images.<BR><BR>
  
*[http://ygac.med.yale.edu/triples/triples.htm TRIPLES- a database of transposon-insertion phenotypes, localization and expression]  
+
*[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.]<BR><BR>
Yeast transposon tagging data from the  [http://ygac.med.yale.edu  Yale Genome Analysis Center.]<BR><BR>
 
  
*[http://www.cbs.umn.edu/yeast/ Yeast Membrane Protein Library]
+
*[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 <i>S. cerevisiae</i><BR><BR>
A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from <i>S. cerevisiae</i><BR><BR>
 
  
*[http://yeastgfp.ucsf.edu/ Yeast GFP Fusion Localization Database]
+
*[http://yeastgfp.yeastgenome.org/ Yeast GFP Fusion Localization Database] <i>S. cerevisiae</i> protein localization data
<i>S. cerevisiae</i> protein localization data
+
from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.<BR><BR>
from the laboratories of Erin O'Shea and Jonathan Weissman at
 
the University of California San Francisco.<BR><BR>
 
  
  
 
=Phenotype Data Resources=
 
=Phenotype Data Resources=
  
*[http://syllabus.syr.edu/bio/seerdman/TTG/ Agria Triterpene Glycoside (TTG) Phenotype Query Page]  
+
*[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 <i>Stenocereus gummosus</i> (common name agria). Pre-publication access provided by Scott Erdman at
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 <i>Stenocereus gummosus</i> (common name
 
agria). Pre-publication access provided by Scott Erdman at
 
 
Syracuse University.<BR><BR>
 
Syracuse University.<BR><BR>
  
*[http://yeast.gi.k.u-tokyo.ac.jp/ The Saccharomyces Cerevisiae Morphological Database (SCMD)]  
+
*[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 <i>et al.</i> (2004) <i>Nucleic Acids Res</i> 32:D319-22.]<br><br>
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 <i>et al.</i> (2004) <i>Nucleic Acids Res</i> 32:D319-22.]<br><br>
 
  
*[http://prophecy.lundberg.gu.se/ PROPHECY]
+
*[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) <i>Proc Natl Acad Sci USA</i> 100:15724-9.]<br><br>
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) <i>Proc Natl Acad Sci USA</i> 100:15724-9.]<br><br>
 
  
*[http://genomics.senescence.info/genes/models.html GenAge]  
+
*[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.<br><br>
GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.<br><br>
 
  
 
=Additional Yeast Research Resources=
 
=Additional Yeast Research Resources=
  
*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains]
+
*[http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html Yeast Deletion Strains] Deletion strains created by the <i>Saccharomyces</i> 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.<BR><BR>
Deletion strains created by the <i>Saccharomyces</i> 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.<BR><BR>
 
  
*[http://depts.washington.edu/~yeastrc/index.html NCRR Yeast Resource Center]
+
*[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.]<BR><BR>
Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]<BR><BR>
 
  
*[http://www.sanger.ac.uk/Teams/Team71/durbin/sgrp/ The Saccharomyces Genome Resequencing Project (SGRP)]
+
*[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 <i>S. cerevisiae</i> and <i>S. paradoxus</i>.<br><br>
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 <i>S. cerevisiae</i> and <i>S. paradoxus</i>.<br><br>
 
  
*[http://www.ysbn.org/ Yeast Systems Biology Network]  
+
*[http://www.ysbn.org/ Yeast Systems Biology Network] Promotes the study of <i>S. cerevisiae</i> systems biology by facilitating
Promotes the study of <i>S. cerevisiae</i> 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.<BR><BR>
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.<BR><BR>
 
  
*[http://www.addgene.org Addgene]
+
*[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.<br><br>
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.<br><br>
 
  
  
 
=Other Resources=
 
=Other Resources=
*[http://www.openhelix.com/sgd SGD Tutorial]
+
*[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.<BR><BR>
Developed by [http://www.openhelix.com/index.shtml OpenHelix], this online tutorial describes navigation of SGD and many features of the database.<BR><BR>
 
  
*[http://www.geneontology.org Gene Ontology]
+
*[http://www.geneontology.org Gene Ontology] Gene Ontology (GO) Consortium home page<BR><BR>
Gene Ontology (GO) Consortium home page<BR><BR>
 
  
*[http://www.genome.ad.jp/kegg/ KEGG]
+
*[http://www.genome.ad.jp/kegg/ KEGG] metabolic reactions and pathways from Kyoto University, Kyoto, Japan<BR><BR>
metabolic reactions and pathways from Kyoto University, Kyoto, Japan<BR><BR>
 
  
*[http://restools.sdsc.edu/ Molecular Biology]
+
*[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.<BR><BR>
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.<BR><BR>
 
  
*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences]
+
*[http://mcb.harvard.edu/BioLinks.html WWW Virtual Library: Biosciences] provided by the Harvard Biolabs<BR><BR>
provided by the Harvard Biolabs<BR><BR>
 
  
*[http://www.microbes.info/ Microbes.info]
+
*[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.<BR><BR>
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.<BR><BR>
 
  
*[http://www.els.net/ Encyclopedia of Life Sciences]
+
*[http://www.els.net/ Encyclopedia of Life Sciences] a collection of articles on a wide variety of biological topics, from the Nature Publishing Group<BR><BR>
a collection of articles on a wide variety of biological topics, from the Nature Publishing Group<BR><BR>
 
  
*[http://dir.yahoo.com/Science/biology/ Yahoo]
+
*[http://dir.yahoo.com/Science/biology/ Yahoo] list of WWW biological information resources<BR><BR>
list of WWW biological information resources<BR><BR>
 
  
*[http://www.nature.com/Scitable Scitable]
+
*[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.<BR><BR>
A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.<BR><BR>
 
  
  

Revision as of 12:15, 18 June 2010

General Yeast Resources

  • 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.

Nucleic Acid Data Resources

  • GenBank sequence repository at the NCBI, Bethesda, Maryland, USA

  • EMBL sequence repository at the EBI, Hinxton Hall, Cambridge, UK

  • DDBJ sequence repository at Mishima, Japan

  • GenePalette software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences

  • OriDB catalog of confirmed and predicted DNA replication origin sites, currently limited to S. cerevisiae

  • Yeast Introns yeast intron data from the Ares Lab, U.C. Santa Cruz

  • Yeast snoRNAs yeast small nucleolar RNA (snoRNA) data from Dmitry A. Samarsky and Maurille J. Fournier, Univ. of Massachusetts

  • Yeast tRNAs yeast tRNA information from Todd Lowe, UC-Santa Cruz

Genome and Protein Resources

  • Yeast Genome Directory A collection of papers describing the sequencing of each chromosome of the S. cerevisiae genome

  • Structural assignments of proteins This website provides structural assignments to protein sequences at the superfamily level. You can browse an overview of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See Gough et al. for more information.

  • Genome Sequence Center: BLAST Serverat 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.

genome/proteome-wide studies, the MIPS database, and BIND.

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 Byrne and Wolfe.

  • 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 Penkett CJ, Morris JA, Wood V, and Bahler J (Wellcome Trust Sanger Institute, Cambridge, UK).

  • iProto Yeast an iPhone application containing proteome information for several

different Saccharomyces and Schizosaccharomyces strains


Expression Data Resources

  • Yeast Cell Cycle Analysis Projects Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies href="/cgi-bin/reference/reference.pl?dbid=S000048277 Spellman et al. (1998) Mol Cell Biol 9:3273-3297.] These data were re-analyzed in: (1) 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. View data, and (2) 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. View data.

  • 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 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.

  • 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 Doniger et al. (2003) Genome Biology 4:R7)

  • Yeast SAGE homepage for Serial Analysis of Gene Expression project at Johns Hopkins University


Localization Data Resources

images.

  • Yeast Membrane Protein Library A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae

from the laboratories of Erin O'Shea and Jonathan Weissman at the University of California San Francisco hosted by SGD.


Phenotype Data Resources

  • 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.

  • GenAge GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.

Additional Yeast Research Resources

  • NCRR Yeast Resource Center Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]

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.

  • Addgene Repository and distributor of plasmid constructs described in published literature. Search for a plasmid or deposit your plasmid to the repository.


Other Resources

  • SGD Tutorial Developed by OpenHelix, this online tutorial describes navigation of SGD and many features of the database.

  • KEGG metabolic reactions and pathways from Kyoto University, Kyoto, Japan

  • 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.

  • Microbes.info The Microbiology Information Portal. This site contains resources, news, and information about many different aspects of microbiology. Its General Microbiology section contains links to various databases, culture collections, genetic analysis sites, and method sites.

  • Yahoo list of WWW biological information resources

  • 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:
2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 |


View SGD's article] for:
2008 | 2007 | 2006 | 2005| 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998