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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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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 [email protected]
