gene ontology at wormbase: making the most of go annotations kimberly van auken
TRANSCRIPT
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/
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
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/
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: [email protected]
Thank you to WormBase, Gene Ontology Consortium, UniProtKBWB- Juancarlos Chan, Sibyl Gao, Kevin Howe
UniProtKB – Tony Sawford, Rachael Huntley (UCL)