Revision as of 18:23, 18 July 2011 by Jodi
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.
- BioSci Yeast Archives search the Yeast Biosci Newsgroup
Nucleic Acid Data Resources
- 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
- PROSPECT: Promoter Inspection Tool explore promoter regions by searching for genes or a sequence. Also contains a list of yeast transcription factor binding sites.
- Regulatory Sequence Analysis Tools search for regulatory signals in the non-coding sequences of S. cerevisiae, S. pombe, and other organisms
- 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 Note that this web site is not exhaustive, and some of the information is outdated.
- Search for conserved patterns in Saccharomyces spp. search tool for identification and analysis of conserved patterns in Saccharomyces promoters. Formore information, please refer to Kohli DK, et al (2004) In Silico Biol 4(3):0034]
- 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.
- Yeast Project at MIPS yeast information from the Munich Information Center for Protein Sequences (MIPS)
- Yeast Proteome Database (YPD) yeast protein information from Incyte Genomics, Inc. Access to this resource requires a subscription.
- 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 Marcotte et al. (1999) Nature 402:83-86.
- TRIPLES - a database of transposon-insertion phenotypes, localization and expression Yeast transposon tagging data from the Yale Genome Analysis Center.
- Yeast Protein Linkage Map The Fields lab's systematic Two-Hybrid project. Results are described in Uetz et al. (2000) Nature 403:623-627.
- 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 MIPS database, and BIND.
- 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 General Repository of Interaction Datasets (BioGRID) and as a result brings a large dataset of interactions to your fingertips.
- 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 Riffle et al. (2005) Nucleic Acids Res 33(Database issue):D378-82 for more information.
- The Global Proteome Machine Database (GPMDB) a database of mass spectrometry based proteomics information, populated by the general proteomics community.
- 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 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
- Yeast Nucleosome Positions a compiled and systematic reference map of nucleosome positions across the S. cerevisiae genome
- InterologFinder A database of conserved and predicted novel protein-protein interactions (interologs or interologues) in human, mouse, fly, worm, and yeast based on interaction of orthologous proteins found in the other organisms. For more information please see Wiles et al., (2010) BMC Syst Biol. Mar 30;4:36..
Expression Data Resources
- 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 Monteiro et al.</a, (2008), Nucleic Acids Research 2008 36(Database issue):D132-D136).
- SCEPTRANS A website for visualizing and studying periodic transcription in yeast (see Kudlicki et al. (2007) Bioinformatics)
- Yeast Cell Cycle Analysis Projects Comprehensive identification of genes whose mRNA levels are regulated by the cell cycle; accompanies 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.
- Yeast Microarray Global Viewer a database containing most of the published yeast microarray expression datasets as described in Marc et al. (2001) Nucleic Acids Res 29(13):e63
- PAM: Prediction Analysis for Microarrays a software tool for interpretation of microarray expression datasets
- 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
- 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 Riffle et al (2010) for more information.
- YeastProtein Localization database (YPL.db) S. cerevisiae protein localization data from University Graz. Users may also submit images.
- TRIPLES- a database of transposon-insertion phenotypes, localization and expression Yeast transposon tagging data from the Yale Genome Analysis Center.
- Yeast Membrane Protein Library A collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from S. cerevisiae
- 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
- 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.
- The Saccharomyces Cerevisiae Morphological Database (SCMD) A collection of micrographs of budding yeast mutants. For more information, please refer to Saito et al. (2004) Nucleic Acids Res 32:D319-22.
- 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 Warringer et al. (2003) Proc Natl Acad Sci USA 100:15724-9.
- GenAge GenAge provides a compiled list of genes associated with aging and longevity in yeast and other model organisms.
Additional Yeast Research Resources
- Yeast Deletion Strains Deletion strains created by the Saccharomyces Genome Deletion project] are available via ATCC (online catalog available), Open Biosystems, and Invitrogen (Research Genetics). The Community Posting Page provided by the Saccharomyces Genome Deletion Project enables users of the mutant collection to share information about the collection. EUROSCARF makes deletion strains available from the EUROFAN projects.
- NCRR Yeast Resource Center Information about services offered by the NCRR Yeast Resource Center at the University of Washington in Seattle.]
- The Saccharomyces Genome Resequencing Project (SGRP) A colloboration between the Sanger Institute and Prof. Ed Louis' group at the Institute of Genetics, University of Nottingham to analyze sequences from multiple strains of S. cerevisiae and S. paradoxus.
- 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.
- Addgene Repository and distributor of plasmid constructs described in published literature. Search for a plasmid or deposit your plasmid to the repository.
- SGD Tutorial Developed by OpenHelix, this online tutorial describes navigation of SGD and many features of the database.
- Gene Ontology Gene Ontology (GO) Consortium home page
- 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.
- WWW Virtual Library: Biosciences provided by the Harvard Biolabs
- 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.
- Encyclopedia of Life Sciences a collection of articles on a wide variety of biological topics, from the Nature Publishing Group
- 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.