Gene Ontology at WormBase: Making the Most of GO Annotations

Kimberly Van Auken

What is the Gene Ontology (GO)?

• A controlled vocabulary for annotating three aspects of a gene product’s biology:

• Biological Process (BP) – the molecular, cellular, and organismal level processes in which a gene product is involved

• Molecular Function (MF) – the molecular activity of a gene product

• Cellular Component (CC) – the subcellular localization of a gene product

What are GO Annotations?

• Human and machine readable associations between genes and GO terms along with supporting metadata– Reference– Contextual Information– Evidence Code (how the association is Inferred)• Mutant Phenotype - IMP• Genetic Interaction - IGI• Direct Assay – IDA

How can you access and use GO annotations in your work?

• Browse on the WormBase gene pages in the Gene Ontology widget

• Browse the ontology and annotations in the WormBase Ontology Browser (WOBr)

• Browse the ontology and annotations; download annotation files for analysis from http://geneontology.org

• Enrichment analysis powered by PANTHER http://pantherdb.org/

GO Annotations on Gene Pages – Gene Ontology Widget

GO Widget –What’s New? Two Views: Summary and Full

GO Widget –Summary View

z

Summary View Includes Annotation Extensions

• What are the transcriptional regulatory targets?

e.g., hsp-3

• Under what conditions does the regulation occur?

e.g., Tunicamycin treatment• Format: Relations Ontology term and

entity e.g., has regulation target hsp-3

Annotation Extensions Provide Contextual Information

Full View Includes Supporting Evidence

How can you access and use GO annotations in your work?

• Browse on the WormBase gene pages in the Gene Ontology widget

• Browse the ontology and annotations in the WormBase Ontology Browser (WOBr)

• Browse the ontology and annotations; download annotation files for analysis from http://geneontology.org

• Enrichment analysis powered by PANTHER http://pantherdb.org/

Browse GO Annotations Using the WormBase Ontology Browser (WOBr)

View Ontology Structure and Find Direct and Inferred Annotations Using WOBr

How can you access and use GO annotations in your work?

• Browse on the WormBase gene pages in the Gene Ontology widget

• Browse the ontology and annotations in the WormBase Ontology Browser (WOBr)

• Browse the ontology and annotations; download annotation files for analysis from http://geneontology.org

• Enrichment analysis powered by PANTHER http://pantherdb.org/

Annotation Files and Enrichment Analysis: Gene Ontology Consortium

http://geneontology.org/

Download Gene Association Files(GAFs)

Perform Enrichment Analysis

How can you access and use GO annotations in your work?

• Browse on the WormBase gene pages in the Gene Ontology widget

• Browse the ontology and annotations in the WormBase Ontology Browser (WOBr)

• Browse the ontology and annotations; download annotation files for analysis from http://geneontology.org

• Enrichment analysis powered by PANTHER http://pantherdb.org/

GO Enrichment Analysis at PANTHER

Upload IDs or files

Select Caenorhabditis

elegans

Statisticaloverrepresentation

test

http://pantherdb.org/

Mi et al., 2013, Nat. Protoc.PMID:23868073

PANTHER Enrichment Analysis Results

http://pantherdb.org/

Enriched GO Terms P values

Annotations and Ontologies are Up-to-Date at PANTHER!!

WB GO Annotation - What’s coming?

• GO Annotation for more nematode genomes• Link out from WB to PANTHER enrichment tool• Community assessment of GO annotations

We value your input! email: help@wormbase.org

Thank you to WormBase, Gene Ontology Consortium, UniProtKBWB- Juancarlos Chan, Sibyl Gao, Kevin Howe

UniProtKB – Tony Sawford, Rachael Huntley (UCL)