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Applications of GO

Applications of GO. Goals of Gene Ontology Project. Goals of Gene Ontology Project. Create controlled vocabularies terms and definitions. Goals of Gene Ontology Project. Create controlled vocabularies terms and definitions Produce annotations to terms gene product -> GO terms.

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Applications of GO

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  1. Applications of GO

  2. Goals of Gene Ontology Project

  3. Goals of Gene Ontology Project • Create controlled vocabularies • terms and definitions

  4. Goals of Gene Ontology Project • Create controlled vocabularies • terms and definitions • Produce annotations to terms • gene product -> GO terms

  5. Goals of Gene Ontology Project • Create controlled vocabularies • terms and definitions • Produce annotations to terms • gene product -> GO terms • Produce GO tools • browsing, searching and editing

  6. Goals of Gene Ontology Project • Create controlled vocabularies • terms and definitions • Produce annotations to terms • gene product -> GO terms • Produce GO tools • browsing, searching and editing • Make everything publicly available

  7. gene product Annotations to GO • ‘Gene associations’ • Associations between a gene/gene product and GO terms • Association made to each of the ontologies cellular component biological process molecular function

  8. Annotations to GO • Three key parts: • gene name/id

  9. Annotations to GO • Three key parts: • gene name/id • GO term

  10. Annotations to GO • Three key parts: • gene name/id • GO term(s) • evidence for association

  11. SPTR O00505 IMA3_HUMAN GO:0006886 GOA:interpro IEA P SPTR O00505 IMA3_HUMAN GO:0005634 GOA:spkw IEA C SPTR O00505 IMA3_HUMAN GO:0005643 PUBMED:9154134 TAS C Importin alpha-3 subunit IPI00012092 protein taxon:9606 20020920 SPTR Importin alpha-3 subunit IPI00012092 protein taxon:9606 20011011 SPTR Importin alpha-3 subunit IPI00012092 protein taxon:9606 20020630 SPTR Gene association file nucleus intracellular protein transport nuclear pore

  12. Types of GO annotation:  Electronic Annotation Manual Annotation

  13. Evidence types • ISS: Inferred from Sequence/structural Similarity • IDA: Inferred from Direct Assay • IPI: Inferred from Physical Interaction • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • IEP: Inferred from Expression Pattern • TAS: Traceable Author Statement • NAS: Non-traceable Author Statement • IC: Inferred by Curator • ND: No Data available • IEA: Inferred from electronic annotation

  14. Evidence types • ISS: Inferred from Sequence/structural Similarity • IDA: Inferred from Direct Assay • IPI: Inferred from Physical Interaction • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • IEP: Inferred from Expression Pattern • TAS: Traceable Author Statement • NAS: Non-traceable Author Statement • IC: Inferred by Curator • ND: No Data available • IEA: Inferred from electronic annotation

  15. Evidence types • ISS: Inferred from Sequence/structural Similarity • IDA: Inferred from Direct Assay • IPI: Inferred from Physical Interaction • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • IEP: Inferred from Expression Pattern • TAS: Traceable Author Statement • NAS: Non-traceable Author Statement • IC: Inferred by Curator • ND: No Data available • IEA: Inferred from electronic annotation

  16. Evidence types • ISS: Inferred from Sequence/structural Similarity • IDA: Inferred from Direct Assay • IPI: Inferred from Physical Interaction • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • IEP: Inferred from Expression Pattern • TAS: Traceable Author Statement • NAS: Non-traceable Author Statement • IC: Inferred by Curator • ND: No Data available • IEA: Inferred from electronic annotation

  17. Evidence types • ISS: Inferred from Sequence/structural Similarity • IDA: Inferred from Direct Assay • IPI: Inferred from Physical Interaction • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • IEP: Inferred from Expression Pattern • TAS: Traceable Author Statement • NAS: Non-traceable Author Statement • IC: Inferred by Curator • ND: No Data available • IEA: Inferred from electronic annotation

  18. Evidence types • ISS: Inferred from Sequence/structural Similarity • IDA: Inferred from Direct Assay • IPI: Inferred from Physical Interaction • IMP: Inferred from Mutant Phenotype • IGI: Inferred from Genetic Interaction • IEP: Inferred from Expression Pattern • TAS: Traceable Author Statement • NAS: Non-traceable Author Statement • IC: Inferred by Curator • ND: No Data available • IEA: Inferred from electronic annotation

  19. Inferred by Electronic Annotation • Annotation derived without human validation • mappings file e.g. interpro2go, ec2go. • Blast search ‘hits’ • Lower ‘quality’ than experimental codes

  20. Fatty acid biosynthesis ( Swiss-Prot Keyword) EC:6.4.1.2 (EC number) IPR000438: Acetyl-CoA carboxylase carboxyl transferase beta subunit (InterPro entry) GO:Fatty acid biosynthesis (GO:0006633) GO:acetyl-CoA carboxylaseactivity (GO:0003989) GO:acetyl-CoA carboxylase activity (GO:0003989) Mappings files

  21. SPTR O00505 IMA3_HUMAN GO:0006886 GOA:interpro IEA P SPTR O00505 IMA3_HUMAN GO:0005634 GOA:spkw IEA C SPTR O00505 IMA3_HUMAN GO:0005643 PUBMED:9154134 TAS C Importin alpha-3 subunit IPI00012092 protein taxon:9606 20020920 SPTR Importin alpha-3 subunit IPI00012092 protein taxon:9606 20011011 SPTR Importin alpha-3 subunit IPI00012092 protein taxon:9606 20020630 SPTR Gene association file using a Swiss-Prot keyword to GO mappings file using an InterPro to GO mappings file

  22. Submitting gene associations • Many model organism databases • Drosophila, mouse,Saccharomyces, rat, zebrafish, prokaryotes, Arabidopsis, slime mould, C. elegans, rice, parasites, viruses • Swiss-Prot (UniProt) • Associations for >8000 species including human

  23. Databases mouse rat UniProt GOA-Human fly man yeast GO parasite plants bacteria worm fish UniProt GOA-SPTR All Species

  24. Finding GO terms In this study, we report the isolation and molecular characterization of the B. napus PERK1 cDNA, that is predicted to encode a novel receptor-like kinase. We have shown that like other plant RLKs, the kinase domain of PERK1 has serine/threonine kinase activity, In addition, the location of a PERK1-GTP fusion protein to the plasma membrane supports the prediction that PERK1 is an integral membrane protein…these kinases have been implicated in early stages of wound response…

  25. GO slims • Restricted view of the ontologies • Give broad view of gene function • Can be organism-specific or generic • plant • mammal • microbe

  26. GO slims

  27. GO for microarray analysis • Annotations give ‘function’ label to genes • Ask meaningful questions of microarray data e.g. • genes involved in the same process, same/different expression patterns?

  28. component process function Gene experimental condition GO for microarray analysis

  29. The tutorial • Part I • Navigating GO and its annotations using • Part II • Analysing microarray data using GO with

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