1 Gene Ontology and Functional Annotation Donghui Li ASPB Plant Biology, June 29, 2008, Merida

2 TAIR literature statistics May 2007May 2008 Reference31,05834,179 Research articles22,64025,001 Full-text papers15,57216,638 Average new papers/month Loci with valid references 9,28910,847

3 Functional annotation Controlled vocabularies: GO and PO Functional annotation at TAIR Community annotation Outline

4 is defined as the process of collecting information about a genes biological identity: molecular function (protein kinase) biological roles (protein phosphorylation) subcellular localization (cytoplasm) aliases mutant phenotype expression domain Functional annotation

5 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 What is an annotation? Adapted from Harold J Drabkin, The Jackson Laboratory

6 Smith et al. (2006) determined by an enzyme 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

7 Non-controlled vocabulary same name, different concept different name, same concept Controlled vocabulary (CV) Controlled vocabulary A standardized restricted set of defined terms designed to reduce ambiguity in describing a concept

8 Same name, different concept Cell

9 Same name, different concept germination seed germination pollen germination spore germination

10 glucose biosynthesis glucose synthesis glucose formation glucose anabolism gluconeogenesis Different name, same concept noncarbohydrate precursors (pyruvate, amino acids and glycerol) glucose (3Z)-phytochromobilin + oxidized ferredoxin = biliverdin IXa + reduced ferredoxin. (EC: ) phytochromobilin synthase activity = phytochromobilin:ferredoxin oxidoreductase activity protein formation translation = protein biosynthesis

11 Cross-species cross-database comparison is problematic without CV translation protein biosynthesis phytochromobilin synthase activity phytochromobilin:ferredoxin oxidoreductase activity

12 Cross-species cross-database comparison is problematic without CV pollenspore germination seed germination pollen germination spore germination

13 GO: The Gene Ontology, Gene Ontology Consortium PO: The Plant Ontology, Plant Ontology Consortium Controlled vocabularies used by TAIR

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

15 Term

16 Ontology structure: directed acyclic graph (DAG) DAG: each child may have one or more parents parent 1 child parent 2

17 protein complex organelle mitochondrion fatty acid beta-oxidation multienzyme complex Ontology structure: directed acyclic graph (DAG)

18 is-a protein complex organelle mitochondrion fatty acid beta-oxidation multienzyme complex part-of is-a Ontology structure: term-term relationships

19 Gene ontology browser: AmiGO

20 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 Plant Ontology

21 term evidence association gene How are annotations made? The Plant Journal (2006) 47:701 AT5G27620 GO: protein kinase activity kinase assay

22 Experimental evidence codes EXP- Inferred from Experiment IMP-IMP IMP- Inferred from Mutant Phenotype IDA-IDA IDA- Inferred from Direct Assay IGI- IGI IGI- Inferred from Genetic Interaction IPI-IPI IPI- Inferred from Physical Interaction IEP-IEP IEP- Inferred from Expression Pattern Computational analysis evidence codes ISS-ISS ISS- Inferred from Sequence or structural Similarity Evidence codes

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24 May 2008 Known Known, EXPUnannotated Unknown Functional annotation of Arabidopsis genome using GO

25 Search GO Annotations

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31 TotalWith gene- related data IndexedCurated Papers in priority 1 journals %144 (86%) Papers in priority 2 journals %207 (54%) Papers in priority 3 journals %31 (10%) Papers in priority 4 journals %11 (2%) Total (30%) Papers entered into TAIR (May 07 to May 08)

32 TAIR - Plant Physiology collaboration Author submits annotation after the paper is accepted Web-based interface AGI locus identifier (At1g01040) Gene function annotation linked to loci with method Will expand to include other journals (Plant Cell...)

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34 Functional annotation submission form

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