annotation of gene function …and how thats useful to you
TRANSCRIPT
Annotation of Gene Function
…and how that’s 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.
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
MethodMethod
Controlled vocabulariesControlled
vocabularies
Gene productGene
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 biosynthesisglucose synthesisglucose formationglucose anabolismgluconeogenesis
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 activitieskinase activity, DNA binding activity
biological process: biological goal or objectivesignal transductionmitosis, purine metabolism
cellular component: location or complexnucleus 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
Publication The Plant Journal (2006) 47:701
Which gene? At5g27620
Annotation
How are annotations made?
Experimental evidence codesExperimental evidence codes
-- IInferred from MMutant PPhenotype (mutant analysis)
-- IInferred from DDirect AAssay ( (enzyme assayenzyme assay))
- I- Inferred from GGenetic IInteraction (double mutant analysis)
-- IInferred from PPhysical IInteraction (yeast 2-H)
-- IInferred from EExpression PPattern ( (Northern blotNorthern blot))
Computational analysisComputational analysis
Author statement
Curatorial statement
Evidence codes
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
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
External links
GO http://www.geneontology.org/
AmiGO http://www.godatabase.org/
PO http://www.plantontology.org/
Questions [email protected]