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Using The Gene Ontology:

Using The Gene Ontology:. Gene Product Annotation. GO Project Goals. Compile structured vocabularies describing aspects of molecular biology Describe gene products using vocabulary terms (annotation) Develop tools: to query and modify the vocabularies and annotations

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Using The Gene Ontology:

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  1. Using The Gene Ontology: Gene Product Annotation

  2. GO Project Goals • Compile structured vocabularies describing • aspects of molecular biology • Describe gene products using vocabulary terms • (annotation) • Develop tools: • to query and modify the vocabularies and • annotations • annotation tools for curators

  3. GO Data • GO provides two bodies of data: • Terms with definitions and cross- • references • Gene product annotations with • supporting data

  4. The Three Ontologies • Molecular Function — elemental activity or task • nuclease, DNA binding, transcription factor • Biological Process — broad objective or goal • mitosis, signal transduction, metabolism • Cellular Component — location or complex • nucleus, ribosome, origin recognition complex

  5. DAG Structure Directed acyclic graph: each child may have one or more parents

  6. The True Path Rule Every path from a node back to the root must be biologically accurate

  7. GO Annotation • Association between gene product and • applicable GO terms • Provided by member databases • Made by manual or automated methods

  8. DAG Structure Annotate to any level within DAG

  9. DAG Structure mitotic chromosome condensation S.c. BRN1, D.m. barren Annotate to any level within DAG

  10. DAG Structure mitosis S.c. NNF1 mitotic chromosome condensation S.c. BRN1, D.m. barren Annotate to any level within DAG

  11. GO Annotation: Data • Database object: gene or gene product • GO term ID • Reference • publication or computational method • Evidence supporting annotation

  12. GO Evidence Codes IDA-Inferred from Direct Assay IMP-Inferred from Mutant Phenotype IGI-Inferred from Genetic Interaction IPI-Inferred from Physical Interaction IEP-Inferred from Expression Pattern TAS-Traceable Author Statement NAS-Non-traceable Author Statement IC - Inferred by Curator ISS-Inferred from Sequence or structural Similarity IEA-Inferred from Electronic Annotation ND-Not Determined

  13. GO Evidence Codes IDA-Inferred from Direct Assay IMP-Inferred from Mutant Phenotype IGI-Inferred from Genetic Interaction IPI-Inferred from Physical Interaction IEP-Inferred from Expression Pattern TAS-Traceable Author Statement NAS-Non-traceable Author Statement IC - Inferred by Curator ISS-Inferred from Sequence or structural Similarity IEA-Inferred from Electronic Annotation ND-Not Determined From primary literature

  14. GO Evidence Codes From reviews or introductions IDA-Inferred from Direct Assay IMP-Inferred from Mutant Phenotype IGI-Inferred from Genetic Interaction IPI-Inferred from Physical Interaction IEP-Inferred from Expression Pattern TAS-Traceable Author Statement NAS-Non-traceable Author Statement IC - Inferred by Curator ISS-Inferred from Sequence or structural Similarity IEA-Inferred from Electronic Annotation ND-Not Determined From primary literature

  15. GO Evidence Codes From reviews or introductions IDA-Inferred from Direct Assay IMP-Inferred from Mutant Phenotype IGI-Inferred from Genetic Interaction IPI-Inferred from Physical Interaction IEP-Inferred from Expression Pattern TAS-Traceable Author Statement NAS-Non-traceable Author Statement IC - Inferred by Curator ISS-Inferred from Sequence or structural Similarity IEA-Inferred from Electronic Annotation ND-Not Determined From primary literature

  16. GO Evidence Codes From reviews or introductions IDA-Inferred from Direct Assay IMP-Inferred from Mutant Phenotype IGI-Inferred from Genetic Interaction IPI-Inferred from Physical Interaction IEP-Inferred from Expression Pattern TAS-Traceable Author Statement NAS-Non-traceable Author Statement IC - Inferred by Curator ISS-Inferred from Sequence or structural Similarity IEA-Inferred from Electronic Annotation ND-Not Determined automated From primary literature

  17. GO Annotation: Methods • Manual • Automated • sequence similarity • transitive annotation • nomenclature, other text matching

  18. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C Encodes Saccharomyces cerevisiae Purine Nucleoside Phosphorylase. J. Bacteriology183(16): 4910-4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles)

  19. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol.183(16): 4910–4913. Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA

  20. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol.183(16): 4910–4913. FUNCTION: Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA purine nucleoside phosphorylase

  21. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C ncodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol.183(16): 4910–4913. FUNCTION: Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA purine nucleoside phosphorylase IMP

  22. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol.183(16): 4910–4913. FUNCTION: Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA purine nucleoside phosphorylase IMP

  23. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol.183(16): 4910–4913. FUNCTION: Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA purine nucleoside phosphorylase PROCESS: purine nucleoside catabolism IMP

  24. Literature-Based Manual Annotation: Experimental Evidence Codes Lecoq, K., et al. (2001) YLR209C encodes Saccharomyces cerevisiae purine nucleoside phosphorylase. J. Bacteriol.183(16): 4910–4913. FUNCTION: Experiment 1 - Purification and enzyme assay Purified His-tagged Ylr209cp; can convert various nucleoside substrates to bases + Pi; inosine and guanosine are substrates Experiment 2 - Knockout of YLR209C null mutant excretes inosine and guanosine into medium (compounds in medium separated by chromatography and identified by HPLC separation profiles) IDA purine nucleoside phosphorylase PROCESS: purine nucleoside catabolism IMP This paper has no data for cellular component.

  25. YFP Automated Annotation: InterPro Example InterPro entry GO entry InterPro2go links InterPro entries and GO terms

  26. YFP Automated Annotation: InterPro Example Run InterProScan to link YFP and InterPro entry InterPro entry GO entry InterPro2go links InterPro entries and GO terms

  27. YFP Automated Annotation: InterPro Example Run InterProScan to link YFP and InterPro entry Infer GO term from the other two links InterPro entry GO entry InterPro2go links InterPro entries and GO terms

  28. detailed view of term AmiGO Browser

  29. gene products annotated to term AmiGO Browser

  30. GO Annotation: Contributors • FlyBase • WormBase • Saccharomyces Genome Database • DictyBase • Mouse Genome Informatics • Gramene • The Arabidopsis Information Resource • Compugen, Inc. • Swiss-Prot/TrEMBL/InterPro • Pathogen Sequencing Unit (Sanger Institute) • PomBase (Sanger Institute) • Rat Genome Database • The Institute for Genomic Research

  31. GO Annotation: Organisms • Fruit fly (Drosophila melanogaster) • Budding yeast (Saccharomyces cerevisiae) • Fission yeast (Schizosaccharomycespombe) • Human (Homosapiens) • Mouse (Mus musculus) • Rice (Oryza sativa) • Rat (Rattusnorvegicus) • Tsetse fly (G. morsitans) • Caenorhabditiselegans • Arabidopsis thaliana • Vibrio cholerae • Dictyostelium discoideum

  32. Current GO Annotations

  33. www.geneontology.org • FlyBase & Berkeley Drosophila Genome Project • WormBase • Saccharomyces Genome Database • DictyBase • Mouse Genome Informatics • Gramene • The Arabidopsis Information Resource • Compugen, Inc. • Swiss-Prot/TrEMBL/InterPro • Pathogen Sequencing Unit (Sanger Institute) • PomBase (Sanger Institute) • Rat Genome Database • Genome Knowledge Base (CSHL) • The Institute for Genomic Research The Gene Ontology Consortium is supported by NHGRI grant HG02273 (R01). The Gene Ontology project thanks AstraZeneca for financial support. The Stanford group acknowledges a gift from Incyte Genomics.

  34. Conference: Standards and Ontologies for Functional Genomics (SOFG) Towards unified ontologies for describing biology and biomedicine 17 – 20 November 2002 Hinxton Hall Conference Centre Hinxton, Cambridge, UK www.wellcome.ac.uk/hinxton/sofg

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