Annotation of Gene Function …and how thats useful to you

What is TAIR*? NSF-funded project begun in 1999 Web resource for Arabidopsis data and stocks Literature-based manual annotation of gene function Genome annotation (gene structure, computational gene function) * URL

Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

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 …based on a particular method …and 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 Method Controlled vocabularies Gene product

Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

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

Different names, 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

Same name, different concepts

Controlled vocabularies (CV) Non-controlled vocabularies Different names, same concept Same name, different concepts A standardized restricted set of defined terms designed to reduce ambiguity in describing a concept Controlled vocabularies Clearly defined Extensive use of synonyms Can be used to perform complex cross-species cross-database queries.

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

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

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

Plant Ontology Plant structure stamen, petal, guard cell Growth and developmental stages seedling growth, rosette growth, leaf development stages, embryo development stages.

Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

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

How are annotations made? What result? Fig. 1: At5g27620 has protein kinase activity What term?[Molecular Function] Protein kinase activity Evidence?Kinase assay PublicationThe Plant Journal (2006) 47:701 Which gene?At5g27620 Annotation

How are annotations made?

Experimental evidence codes -IMP - Inferred from Mutant Phenotype (mutant analysis) -IDA (enzyme assay) - Inferred from Direct Assay (enzyme assay) - IGI - Inferred from Genetic Interaction (double mutant analysis) -IPI - Inferred from Physical Interaction (yeast 2-H) -IEP (Northern blot) - Inferred from Expression Pattern (Northern blot) Computational analysis Author statement Curatorial statement Evidence codes

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

Overview Functional annotation Controlled vocabularies Functional annotation at TAIR Resources and tools at TAIR

GO at TAIR Gene search Keyword search GO annotation search Bulk download Community annotations

Gene Search Finding genes based on controlled vocabulary annotations

Gene search Search by AGI identifier

Gene search results page

Search by gene name Gene search Search by gene name Plant U-box17

Gene search results page

Locus detail page

Annotation detail page

Keyword Search Finding all types of data associated with a given keyword

Select keyword search

Keyword search page

Keyword search result page

Keyword search page

GO Annotation Search Finding GO annotations for sets of genes and grouping them by function, location and biological roles

Select GO annotations

GO annotation search page

Functional categorization

Pie chart for functional annotations

GO annotation search page

Accessing Whole Genome Files When you want it all

Bulk download

GO annotation user submission

GO annotation user submission

External links GOhttp:// AmiGOhttp:// POhttp://