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Using the Gene Ontology. What is GO and why do we need it? How are GO annotations made? Which species are annotated? What can a biologists do with GO?. What is GO and why do we need it?. Defined consistent descriptions (Controlled vocabulary) Dynamic (evolve to include new concepts)

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using the gene ontology
Using the Gene Ontology
  • What is GO and why do we need it?
  • How are GO annotations made?
  • Which species are annotated?
  • What can a biologists do with GO?
what is go and why do we need it
What is GO and why do we need it?
  • Defined consistent descriptions (Controlled vocabulary)
  • Dynamic (evolve to include new concepts)
  • Cross species querying (species independent)
  • Describe biology at different levels of detail
  • Support inherent complexity of the data
slide3

what a gene product does

Acetyl-CoA

CoA-SH

Citrate synthase

TCA

Cycle

Biological Process:

Broad objective or goal

6286 S. pombe

172695 All

Location or Complex

8398 S. pombe

168539 All

5506 S. pombe

151163 All

MolecularFunction:

Cellular Component:

anatomy of a go term
Anatomy of a GO term
  • termname tricarboxylic acid cycle
  • synonym(s) TCA cycle, citric acid cycle, Krebs cycle
  • Definition A nearly universal metabolic pathway in which the acetyl group of …..
  • ID GO:0006099

~17500 terms

slide5

QuickGO browser

www.ebi.ac.uk/ego

Molecular function

DAG, similar to a hierarchy

Except it allows individual child terms to have many parents

Broader parents give rise to more specific children

When a gene is annotated to a term it is automatically annotated to all of its parents……

Concurrent terms

slide6

…..True Path rule

Every possible path from any term back to the root node

must be biologically accurate, or the ontology must be revised

Allows curators to assign terms

at different levels of granularity,

depending what is known or can

be inferred

evidence codes
Evidence Codes
  • IDA inferred from direct assay
  • IPI inferred from physical interaction
  • IGI inferred from genetic interaction
  • TAS traceable author statement
  • IC inferred by curator
  • ISS inferred from sequence similarity
  • IEA from electronic annotation
slide9

How are GO annotations made?S. pombe Curation Strategy

Manual Curation

  • Emphasis on Primary Literature

(IDA, IMP, IGI, IPI, TAS)

  • Manual inspection of sequence similarity (ISS)

Computational Mappings (IEA)

  • InterPro to GO
  • UniProt (Swissprot keyword to GO)
  • Pombe keyword to GO
  • E.C. to GO

1117 PMIDs

3685 annotations

5725 annotations

10360 annotations

so what can biologists do with it
So what can biologists do with it?

Data searching

  • By individual gene
  • By GO term (concept)
  • By sequence

Data analysis

  • By Binning (GO slim/comparative GO slim)
  • By gene list Clustering/looking for overrepresented terms
slide11

By gene…..

Cps1 has annotations to all 3 ontologies

Has multiple process and component

Evidence

code

Attribution

Links to Amigo

www.genedb.org/genedb/pombe

slide12

Number of S. pombe gene products with annotations in each ontology

By GO term (concept)...

Search by term or product

Filter by organism or evidence

slide14

Clicking on the term name/ID takes you to

Term details and annotations

slide17

By Binning…

Unknown process S. pombe 1064 S. cerevisiae 1793

summary
Summary
  • Provides a standard for annotation
  • Allows experimental work to be evaluated in the context of other experimental data which may be annotated at different levels of granularity
  • Allows biolgigts to search and analyse data
  • Becomes incresingly poweful as the ontologies and annotations are refined
acknowledgements
Acknowledgements
  • Help with the annotation
  • Martin Aslett (GeneDB and GO technical support)
  • Lynda Groocock (mitochondrial annotation)
  • GO editorial office
  • SGD staff

GeneDB programmers, support of the GO data in GeneDB

  • Adrian Tivey
  • Arnaud Kerhornou
  • Paul Mooney
  • GeneDB www.genedb.org/
  • QuickGO www.ebi.ac.uk/ego
  • GO www.geneontology.org
  • Amigo www.godatabase.orgcgi-bin/amigo