1. Gene Ontology at WormBase: Making the Most of GO Annotations Kimberly Van Auken

2. 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

3. 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

4. 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 http://geneontology.org Enrichment analysis powered by PANTHER http://pantherdb.org/ http://pantherdb.org/

5. GO Annotations on Gene Pages – Gene Ontology Widget

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

7. GO Widget –Summary View z z

8. 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

9. Full View Includes Supporting Evidence

10. 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 http://geneontology.org Enrichment analysis powered by PANTHER http://pantherdb.org/ http://pantherdb.org/

11. Browse GO Annotations Using the WormBase Ontology Browser (WOBr)

12. View Ontology Structure and Find Direct and Inferred Annotations Using WOBr

13. 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 http://geneontology.org Enrichment analysis powered by PANTHER http://pantherdb.org/ http://pantherdb.org/

14. Annotation Files and Enrichment Analysis: Gene Ontology Consortium http://geneontology.org/ Download Gene Association Files (GAFs) Perform Enrichment Analysis

15. 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 http://geneontology.org Enrichment analysis powered by PANTHER http://pantherdb.org/ http://pantherdb.org/

16. GO Enrichment Analysis at PANTHER Upload IDs or files Select Caenorhabditis elegans Statistical overrepresentation test http://pantherdb.org/ Mi et al., 2013, Nat. Protoc. PMID:23868073

17. PANTHER Enrichment Analysis Results http://pantherdb.org/ Enriched GO Terms P values Annotations and Ontologies are Up-to-Date at PANTHER!!

18. 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, UniProtKB WB- Juancarlos Chan, Sibyl Gao, Kevin Howe UniProtKB – Tony Sawford, Rachael Huntley (UCL)