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Gene function annotation

Gene function annotation. Outline. Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR. Outline. Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR. What is an annotation?.

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Gene function annotation

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  1. Gene function annotation

  2. Outline • Functional annotation • Controlled vocabularies • Functional annotation at TAIR • Resources and tools at TAIR

  3. Outline • Functional annotation • Controlled vocabularies • Functional annotation at TAIR • Resources and tools at TAIR

  4. What is an annotation? An annotation is a statement that a gene product … …has a particular molecular function …is involved in a particular biological process …is located within a certain cellular component …as determined by a particular method …as described in a particular reference. Evidence code Gene product Reference Smith et al. (2006) determined by a direct assay that Abc2 has protein kinase activity, is involved in the process of protein phosphorylation, and is located in the cytoplasm. Controlled vocabularies Adapted from Harold J Drabkin, The Jackson Laboratory

  5. Outline • Functional annotation • Controlled vocabularies • Functional annotation at TAIR • Resources and tools at TAIR

  6. Controlled vocabularies (CV) A standardized restricted set of defined terms designed to reduce ambiguity in describing a concept Non-controlled vocabularies • Different name, same concept • Same name, different concept

  7. Different name, same concept The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol • glucose biosynthesis • glucose synthesis • glucose formation • glucose anabolism • gluconeogenesis

  8. Same name, different concept

  9. Controlled vocabularies (CV) • Clearly defined • Can be used to perform complex cross-species cross-database queries. • What protein kinases are involved in ethylene signaling and are expressed in nucleus?

  10. Controlled vocabularies used at TAIR • The Gene Ontology (GO) vocabularies by the Gene Ontology Consortium • The Plant Ontology (PO) vocabularies by the Plant Ontology Consortium

  11. Gene Ontology molecular function: catalytic / binding activities kinase activity, DNA binding activity biological process: biological goal or objective signal transduction mitosis, purine metabolism cellular component: location or complex nucleus ribosome, proteasome

  12. Relationships: is_a and part_of protein complex organelle is-a is-a mitochondrion part-of-a fatty acid beta-oxidation multienzyme complex

  13. Plant Ontology Plant structure morphological and anatomical structures stamen, petal, guard cell Growth and developmental stages whole plant growth stages and plant structure developmental stages seedling growth, rosette growth, leaf development stages, embryo development stages.

  14. Outline • Functional annotation • Controlled vocabularies • Functional annotation at TAIR • Resources and tools at TAIR

  15. How are annotations made? • Sources • - Primary literature • - Computational analyses of the genome sequence • Contributions from the research community

  16. How are annotations made? Publication The Plant Journal (2006) 47:701 which gene? result/term evidence association AT5G27620

  17. How are annotations made? publication which gene? result/term evidence association Search gene ontology for the most appropriate term(s): protein kinase activity

  18. How are annotations made?

  19. Evidence codes Experimental evidence codes -Inferred from Mutant Phenotype -Inferred from Direct Assay - Inferred from Genetic Interaction -Inferred from Physical Interaction -Inferred from Expression Pattern Computational analysis IEA - Inferred from Electronic Annotation RCA - Reviewed Computational Analysis ISS -Inferred from Sequence Similarity Author statement TAS -Traceable Author Statement NAS -Non-traceable Author Statement Curatorial statement IC -Inferred by Curator ND -No biological Data available

  20. Summary of functional annotation of the Arabidopsis genome Molecular Function Biological Process Cellular component Based on annotation data as of May 3, 2007. More information can be found on TAIR: Portals: Genome Annotation: Genome Snapshot.

  21. Outline • Functional annotation • Controlled vocabularies • Functional annotation at TAIR • Resources and tools at TAIR

  22. GO at TAIR • Gene search • Keyword search • GO annotation search • Bulk download • Community annotations

  23. Gene search: find GO annotations for a gene

  24. Gene search Search by AGI identifier

  25. Gene search results page

  26. Gene search Search by gene name Search by gene name

  27. Gene search results page

  28. Locus detail page

  29. Annotation detail page

  30. Keyword search: find genes associated with a GO or PO term

  31. Select keyword search

  32. Keyword search page

  33. Keyword search result page

  34. Keyword search page

  35. GO annotations search: find GO annotations for sets of genes and group them by function, location and biological roles

  36. Select GO annotations

  37. GO annotation search page

  38. Functional categorization

  39. Pie chart for functional annotations

  40. GO annotation search page

  41. Bulk download

  42. GO annotations user submission

  43. GO annotations user submission curator@arabidopsis.org

  44. External links GO http://www.geneontology.org/ AmiGO http://www.godatabase.org/ QuickGO http://www.ebi.ac.uk/ego/ POhttp://www.plantontology.org/ Questionscurator@arabidopsis.org

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