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. Adapted from Harold J Drabkin, The Jackson Laboratory 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. Reference Evidence code Evidence code Controlled vocabularies Gene product

5 Outline  Functional annotation  Controlled vocabularies  Functional annotation at TAIR  Resources and tools at TAIR

6 Controlled vocabularies (CV) Non-controlled vocabularies  Different name, same concept  Same name, different concept A standardized restricted set of defined terms designed to reduce ambiguity in describing a 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 is-a protein complex organelle mitochondrion fatty acid beta-oxidation multienzyme complex part-of-a is-a Relationships: is_a and part_of

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? AT5G27620 result/term evidence association PublicationThe Plant Journal (2006) 47:701 which gene?

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

18 How are annotations made?

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

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

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 Search by gene name Gene search 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

44 External links GOhttp:// AmiGOhttp:// QuickGOhttp:// POhttp://