1 Gene function annotation. 2 Outline Functional annotation Controlled vocabularies Functional...

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Gene function annotation

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Outline

Functional annotation

Controlled vocabularies

Functional annotation at TAIR

Resources and tools at TAIR

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Outline

Functional annotation

Controlled vocabularies

Functional annotation at TAIR

Resources and tools at TAIR

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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.

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.

ReferenceReference

Evidence code

Evidence code

Controlled vocabulariesControlled

vocabularies

Gene productGene

product

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Outline

Functional annotation

Controlled vocabularies

Functional annotation at TAIR

Resources and tools at TAIR

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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

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Different name, same concept

The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol

glucose biosynthesisglucose synthesisglucose formationglucose anabolismgluconeogenesis

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Same name, different concept

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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?

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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

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Gene Ontology

molecular function: catalytic / binding activitieskinase activity, DNA binding activity

biological process: biological goal or objectivesignal transductionmitosis, purine metabolism

cellular component: location or complexnucleus ribosome, proteasome

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is-a

protein complex

organelle

mitochondrion

fatty acid beta-oxidation multienzyme complex

part-of-a

is-a

Relationships: is_a and part_of

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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.

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Outline

Functional annotation

Controlled vocabularies

Functional annotation at TAIR

Resources and tools at TAIR

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How are annotations made?

Sources

- Primary literature- Computational analyses of the genome sequence- Contributions from the research community

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How are annotations made?

AT5G27620

result/term

evidence

association

Publication The Plant Journal (2006) 47:701

which gene?

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How are annotations made?

Search gene ontology for the most appropriate term(s): protein kinase activity

result/term

evidence

association

publication

which gene?

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How are annotations made?

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Experimental evidence codesExperimental evidence codes

-- IInferred from MMutant PPhenotype

-- IInferred from DDirect AAssay

- I- Inferred from GGenetic IInteraction

-- IInferred from PPhysical IInteraction

-- IInferred from EExpression PPattern

Computational analysisComputational analysis

IEAIEA - I- Inferred from EElectronic AAnnotation

RCARCA - R- Reviewed CComputational AAnalysis

ISSISS -- IInferred from SSequence SSimilarity

Author statement

TASTAS -- TTraceable AAuthor SStatement

NASNAS -- NNon-traceable AAuthor SStatement

Curatorial statement

ICIC -- IInferred by CCurator

NDND -- NNo biological DData available

Evidence codes

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Summary of functional annotation of the Arabidopsis genome

Based on annotation data as of May 3, 2007. More information can be found on TAIR: Portals: Genome Annotation: Genome Snapshot.

Molecular Function Biological Process Cellular component

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Outline

Functional annotation

Controlled vocabularies

Functional annotation at TAIR

Resources and tools at TAIR

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GO at TAIR

Gene search Keyword search GO annotation search Bulk download Community annotations

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Gene search: find GO annotations for a gene

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Gene searchSearch by AGI identifier

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Gene search results page

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Search by gene name Gene searchSearch by gene name

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Gene search results page

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Locus detail page

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Annotation detail page

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

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Select keyword search

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Keyword search page

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Keyword search result page

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Keyword search page

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

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Select GO annotations

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GO annotation search page

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Functional categorization

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Pie chart for functional annotations

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GO annotation search page

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Bulk download

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GO annotations user submission

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curator@arabidopsis.org

GO annotations user submission

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External links

GO http://www.geneontology.org/

AmiGO http://www.godatabase.org/QuickGO http://www.ebi.ac.uk/ego/

PO http://www.plantontology.org/

Questions curator@arabidopsis.org