Difference between revisions of "PMID:19906697"

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{|  id="J4d2f37aff4086"  class=" tableEdit PMID_info_table" 
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'''Engel, SR, Balakrishnan, R, Binkley, G, Christie, KR, Costanzo, MC, Dwight, SS, Fisk, DG, Hirschman, JE, Hitz, BC, Hong, EL, Krieger, CJ, Livstone, MS, Miyasato, SR, Nash, R, Oughtred, R, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Dolinski, K, Botstein, D and Cherry, JM'''  (2010) Saccharomyces Genome Database provides mutant phenotype data.''Nucleic Acids Res.'' '''38''':D433-6
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!align=left  |Abstract
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The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD.
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*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19906697 PubMed]
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*Online version:[http://dx.doi.org/10.1093/nar/gkp917 10.1093/nar/gkp917]
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*[http://yeastgenome.org/cache/PhenotypeTree.html Hierarchical List of Observables]
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*[http://wiki.yeastgenome.org/index.php/Commonly_used_strains Commonly used strains]
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*[http://www.ebi.ac.uk/chebi/ CHEBI]
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*[http://downloads.yeastgenome.org/pub/yeast/literature_curation/phenotype_data.tab Phenotype data download]
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!align=left  |Keywords
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Computational Biology; DNA, Fungal; Databases, Genetic; Databases, Nucleic Acid; Databases, Protein; Genes, Fungal; Genome, Fungal; Information Storage and Retrieval; Internet; Mutation; Phenotype; Protein Structure, Tertiary; Saccharomyces cerevisiae; Software
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==What phenotypes are displayed in SGD? ==
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*Single mutant phenotypes for every gene in the yeast genome
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*"representative" phenotypes
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**classical yeast phenotypes from pivotal papers
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**phenotypes from newly published papers
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*Genetic interactions
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**Suppression
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**Complementation
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**Synthetic lethality
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*Data from large scale screens for genetic interactions
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**Synthetic Genetic Analysis
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**Diploid-based Synthetic Lethality Analysis on Microarrays
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== What is not recorded? ==
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*Mutant phenotypes inferred from assays performed ''in vitro'' or ''in organello''
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*SGD does not curate every possible phenotype from every paper
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==How are the phenotype data recorded?==
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*tabular format
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*controlled vocabularies
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**an "observable"- main feature of the phenotype
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**a "qualifier"- describes the direction or type of change relative to the wild type
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*Interaction data are recorded in BioGRID
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*Additional aspects of the phenotype are also described using controlled vocabularies
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**mutant type (causal mutation)
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**conditions of its occurance (strain background)
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**assay preformed (experiment type, chemicals)
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==How are these phenotype data accessed by users?==
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*Search via the SGD Search
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*Expanded Phenotype Search
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*Advanced Search (using multiple criteria)- displays a list of genes that when mutated share a common phenotype
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==Other tools available on each phenotype page?==
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*"Analyze Gene List" link leads to tools for further analysis
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**GO Term Finder
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**GO Slim Mapper
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**View GO Annotation Summary
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**Download Data
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**Download Options
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==Notes==
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==References==
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{{RefHelp}}
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<references/>
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[[Category:Publication]]
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[[Category:To Be Converted]]

Latest revision as of 12:09, 22 June 2011

Citation

Engel, SR, Balakrishnan, R, Binkley, G, Christie, KR, Costanzo, MC, Dwight, SS, Fisk, DG, Hirschman, JE, Hitz, BC, Hong, EL, Krieger, CJ, Livstone, MS, Miyasato, SR, Nash, R, Oughtred, R, Park, J, Skrzypek, MS, Weng, S, Wong, ED, Dolinski, K, Botstein, D and Cherry, JM (2010) Saccharomyces Genome Database provides mutant phenotype data.Nucleic Acids Res. 38:D433-6

Abstract

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD.

Links
Keywords

Computational Biology; DNA, Fungal; Databases, Genetic; Databases, Nucleic Acid; Databases, Protein; Genes, Fungal; Genome, Fungal; Information Storage and Retrieval; Internet; Mutation; Phenotype; Protein Structure, Tertiary; Saccharomyces cerevisiae; Software

edit table

What phenotypes are displayed in SGD?

  • Single mutant phenotypes for every gene in the yeast genome
  • "representative" phenotypes
    • classical yeast phenotypes from pivotal papers
    • phenotypes from newly published papers
  • Genetic interactions
    • Suppression
    • Complementation
    • Synthetic lethality
  • Data from large scale screens for genetic interactions
    • Synthetic Genetic Analysis
    • Diploid-based Synthetic Lethality Analysis on Microarrays

What is not recorded?

  • Mutant phenotypes inferred from assays performed in vitro or in organello
  • SGD does not curate every possible phenotype from every paper

How are the phenotype data recorded?

  • tabular format
  • controlled vocabularies
    • an "observable"- main feature of the phenotype
    • a "qualifier"- describes the direction or type of change relative to the wild type
  • Interaction data are recorded in BioGRID
  • Additional aspects of the phenotype are also described using controlled vocabularies
    • mutant type (causal mutation)
    • conditions of its occurance (strain background)
    • assay preformed (experiment type, chemicals)

How are these phenotype data accessed by users?

  • Search via the SGD Search
  • Expanded Phenotype Search
  • Advanced Search (using multiple criteria)- displays a list of genes that when mutated share a common phenotype

Other tools available on each phenotype page?

  • "Analyze Gene List" link leads to tools for further analysis
    • GO Term Finder
    • GO Slim Mapper
    • View GO Annotation Summary
    • Download Data
    • Download Options

Notes

References

See Help:References for how to manage references in omp dev.

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