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Using the Gene Ontology

Using the Gene Ontology. What is GO and why do we need it? How are GO annotations made? Which species are annotated? What can a biologists do with GO?. What is GO and why do we need it?. Defined consistent descriptions (Controlled vocabulary) Dynamic (evolve to include new concepts)

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Using the Gene Ontology

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  1. Using the Gene Ontology • What is GO and why do we need it? • How are GO annotations made? • Which species are annotated? • What can a biologists do with GO?

  2. What is GO and why do we need it? • Defined consistent descriptions (Controlled vocabulary) • Dynamic (evolve to include new concepts) • Cross species querying (species independent) • Describe biology at different levels of detail • Support inherent complexity of the data

  3. what a gene product does Acetyl-CoA CoA-SH Citrate synthase TCA Cycle Biological Process: Broad objective or goal 6286 S. pombe 172695 All Location or Complex 8398 S. pombe 168539 All 5506 S. pombe 151163 All MolecularFunction: Cellular Component:

  4. Anatomy of a GO term • termname tricarboxylic acid cycle • synonym(s) TCA cycle, citric acid cycle, Krebs cycle • Definition A nearly universal metabolic pathway in which the acetyl group of ….. • ID GO:0006099 ~17500 terms

  5. QuickGO browser www.ebi.ac.uk/ego Molecular function DAG, similar to a hierarchy Except it allows individual child terms to have many parents Broader parents give rise to more specific children When a gene is annotated to a term it is automatically annotated to all of its parents…… Concurrent terms

  6. …..True Path rule Every possible path from any term back to the root node must be biologically accurate, or the ontology must be revised Allows curators to assign terms at different levels of granularity, depending what is known or can be inferred

  7. http://www.geneontology.org

  8. Evidence Codes • IDA inferred from direct assay • IPI inferred from physical interaction • IGI inferred from genetic interaction • TAS traceable author statement • IC inferred by curator • ISS inferred from sequence similarity • IEA from electronic annotation

  9. How are GO annotations made?S. pombe Curation Strategy Manual Curation • Emphasis on Primary Literature (IDA, IMP, IGI, IPI, TAS) • Manual inspection of sequence similarity (ISS) Computational Mappings (IEA) • InterPro to GO • UniProt (Swissprot keyword to GO) • Pombe keyword to GO • E.C. to GO 1117 PMIDs 3685 annotations 5725 annotations 10360 annotations

  10. So what can biologists do with it? Data searching • By individual gene • By GO term (concept) • By sequence Data analysis • By Binning (GO slim/comparative GO slim) • By gene list Clustering/looking for overrepresented terms

  11. By gene….. Cps1 has annotations to all 3 ontologies Has multiple process and component Evidence code Attribution Links to Amigo www.genedb.org/genedb/pombe

  12. Number of S. pombe gene products with annotations in each ontology By GO term (concept)... Search by term or product Filter by organism or evidence

  13. + will expand a term to show its children

  14. Clicking on the term name/ID takes you to Term details and annotations

  15. Can select sequences based on functional annotation Scrolling down V V V

  16. Search returns children

  17. By Binning… Unknown process S. pombe 1064 S. cerevisiae 1793

  18. Summary • Provides a standard for annotation • Allows experimental work to be evaluated in the context of other experimental data which may be annotated at different levels of granularity • Allows biolgigts to search and analyse data • Becomes incresingly poweful as the ontologies and annotations are refined

  19. Acknowledgements • Help with the annotation • Martin Aslett (GeneDB and GO technical support) • Lynda Groocock (mitochondrial annotation) • GO editorial office • SGD staff GeneDB programmers, support of the GO data in GeneDB • Adrian Tivey • Arnaud Kerhornou • Paul Mooney • GeneDB www.genedb.org/ • QuickGO www.ebi.ac.uk/ego • GO www.geneontology.org • Amigo www.godatabase.orgcgi-bin/amigo

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