1. Applications of GO

2. Goals of Gene Ontology Project

3. 1. Create controlled vocabularies – terms and definitions

4. Goals of Gene Ontology Project 1. Create controlled vocabularies – terms and definitions 2. Produce annotations to terms – gene product -> GO terms

5. Goals of Gene Ontology Project 1. Create controlled vocabularies – terms and definitions 2. Produce annotations to terms – gene product -> GO terms 3. Produce GO tools – browsing, searching and editing

6. Goals of Gene Ontology Project 1. Create controlled vocabularies – terms and definitions 2. Produce annotations to terms – gene product -> GO terms 3. Produce GO tools – browsing, searching and editing Make everything publicly available

7. Annotations to GO ‘Gene associations’ Associations between a gene/gene product and GO terms Association made to each of the ontologies gene product 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. Gene association file Importin alpha-3 subunitIPI00012092 protein taxon:9606 20020920 SPTR Importin alpha-3 subunitIPI00012092 protein taxon:9606 20011011 SPTR Importin alpha-3 subunitIPI00012092 protein taxon:9606 20020630 SPTR SPTRO00505IMA3_HUMANGO:0006886 GOA:interpro IEA P SPTRO00505IMA3_HUMANGO:0005634 GOA:spkw IEA C SPTRO00505IMA3_HUMANGO:0005643 PUBMED:9154134 TAS C intracellular protein transport nucleus 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. Mappings files 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 carboxylase activity ( GO:0003989 ) GO:acetyl-CoA carboxylase activity (GO:0003989)

21. Gene association file Importin alpha-3 subunitIPI00012092 protein taxon:9606 20020920 SPTR Importin alpha-3 subunitIPI00012092 protein taxon:9606 20011011 SPTR Importin alpha-3 subunitIPI00012092 protein taxon:9606 20020630 SPTR SPTRO00505IMA3_HUMANGO:0006886 GOA:interpro IEA P SPTRO00505IMA3_HUMANGO:0005634 GOA:spkw IEA C SPTRO00505IMA3_HUMANGO:0005643 PUBMED:9154134 TAS C using an InterPro to GO mappings file using a Swiss-Prot keyword 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 UniProt GOA-Human GO fly yeast worm man mouserat plants parasite bacteria 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. GO for microarray analysis experimental condition Gene component process function

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