1 Gene function annotation. 2 Outline  Functional annotation  Controlled vocabularies  Functional annotation at TAIR  Resources and tools at TAIR

Download 1 Gene function annotation. 2 Outline  Functional annotation  Controlled vocabularies  Functional annotation at TAIR  Resources and tools at TAIR

Post on 14-Jan-2016

221 views

Category:

Documents

3 download

Embed Size (px)

TRANSCRIPT

  • Gene function annotation

  • Outline Functional annotation

    Controlled vocabularies

    Functional annotation at TAIR

    Resources and tools at TAIR

  • Outline 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 processis located within a certain cellular componentas 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.ReferenceEvidence codeControlled vocabulariesGene product

  • Outline Functional annotation

    Controlled vocabularies

    Functional annotation at TAIR

    Resources and tools at TAIR

  • Controlled vocabularies (CV) Non-controlled vocabularies

    Different name, same conceptSame name, different conceptA standardized restricted set of defined terms designed to reduce ambiguity in describing a concept

  • Different name, same concept glucose biosynthesisglucose synthesisglucose formationglucose anabolismgluconeogenesis

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

  • Same name, different concept

  • 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?

  • 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 Ontologymolecular function: catalytic / binding activitieskinase activity, DNA binding activity

    biological process: biological goal or objectivesignal transductionmitosis, purine metabolism

    cellular component: location or complexnucleus ribosome, proteasome

  • Relationships: is_a and part_ofis-aprotein complexorganellemitochondrionfatty acid beta-oxidation multienzyme complexpart-of-ais-a

  • Plant OntologyPlant 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.

  • Outline 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?AT5G27620result/termevidenceassociationPublicationThe Plant Journal (2006) 47:701which gene?

  • How are annotations made?Search gene ontology for the most appropriate term(s): protein kinase activityresult/termevidenceassociationpublicationwhich gene?

  • How are annotations made?

  • Experimental evidence codes- Inferred from Mutant Phenotype- Inferred from Direct Assay - Inferred from Genetic Interaction- Inferred from Physical Interaction- Inferred from Expression Pattern Computational analysisIEA- Inferred from Electronic AnnotationRCA- Reviewed Computational Analysis ISS- Inferred from Sequence SimilarityAuthor statementTAS- Traceable Author StatementNAS- Non-traceable Author StatementCuratorial statementIC- Inferred by CuratorND- No biological Data availableEvidence codes

  • Summary of functional annotation of the Arabidopsis genomeBased 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

  • Outline Functional annotation

    Controlled vocabularies

    Functional annotation at TAIR

    Resources and tools at TAIR

  • GO at TAIRGene searchKeyword searchGO annotation searchBulk downloadCommunity annotations

  • Gene search: find GO annotations for a gene

  • Gene searchSearch by AGI identifier

  • Gene search results page

  • Gene searchSearch by gene name Search by gene name

  • Gene search results page

  • Locus detail page

  • Annotation detail page

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

  • Select keyword search

  • Keyword search page

  • Keyword search result page

  • Keyword search page

  • GO annotations search: find GO annotations for sets of genes and group 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

  • Bulk download

  • GO annotations user submission

  • curator@arabidopsis.orgGO annotations user submission

  • External linksGOhttp://www.geneontology.org/

    AmiGOhttp://www.godatabase.org/QuickGOhttp://www.ebi.ac.uk/ego/

    POhttp://www.plantontology.org/

    Questionscurator@arabidopsis.org

    Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.

    What is functional annotation;

    I will also introduce controlled vocabularies and gene ontology;

    This is followed by a brief introduction to the current status of functional annotation at TAIR;

    Finally I will demonstrate how to use the tools available at TAIR to find functions of Arabidopsis genes.

    Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.So what is an annotation: An annotation is a statement that a gene producthas a particular molecular functionis involved in a particular biological processis located within a certain cellular componentas determined by a particular method as described in a particular reference.To give you a simple example. An annotation would look like this: Smith et al. 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.Each annotation contains 4 pieces of information: 1) The gene product; 2)Vocabularies or terms that are used to describe the biological identity of the gene product; 3) An evidence code that indicates how the association between the gene product and the terms are made; 4)And finally a reference.The key to high quality annotations is to use standardized controlled vocabularies or terms to describe various aspects of a gene product. For example, in this annotation we used terms such as kinase activity protein phosphorylation cytoplasmto describe Abc2.

    Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.Presentation of GO annotations: when created and why. What they are and how they are used. Also presentation of how GO is being used at TAIR.GO is the designation of a project as well as the product of the project.

    Starting with the cellular level, we are not distinguishing cell types, organs,etc.

    Gene Ontology is a collaboration between the fly (FlyBase), mouse (MGD) genome databases, and yeast (SGD). All three groups had started independent projects to produce controlled vocabularies for the biology of their organisms.

    You will all be familiar with hierarchical system to classify enzymes (EC) or functions (YPD, SwissPROT, MIPS, ).

    We have divided our project into the creation of three ontologies. These are not necessarily hierarchical rather they can be a network of associations -- a directed acyclic graph (DAG).

    Process: cell cycle, nutrient transport, behavior, Function: alcohol dehydrogenase, Cellular Location: organelle, protein complex, subcellular compartmentGO is the designation of a project as well as the product of the project.

    Starting with the cellular level, we are not distinguishing cell types, organs,etc.

    Gene Ontology is a collaboration between the fly (FlyBase), mouse (MGD) genome databases, and yeast (SGD). All three groups had started independent projects to produce controlled vocabularies for the biology of their organisms.

    You will all be familiar with hierarchical system to classify enzymes (EC) or functions (YPD, SwissPROT, MIPS, ).

    We have divided our project into the creation of three ontologies. These are not necessarily hierarchical rather they can be a network of associations -- a directed acyclic graph (DAG).

    Process: cell cycle, nutrient transport, behavior, Function: alcohol dehydrogenase, Cellular Location: organelle, protein complex, subcellular compartmentPlant structure

    A controlled vocabulary of botanical terms describing morphological and anatomical structures representing organ, tissue

Recommended

View more >