1. Overview Gene Ontology Introduction Biological network data
Text mining
Gene Ontology
Expression data basics
Expression, text mining, and GO
Modules and complexes
Domains and conclusion

2. Gene Ontology
What is Gene Ontology?
How can Gene Ontology be used?

3. What is Gene Ontology (GO)?
Controlled vocabulary for describing genes, starting with three root terms
Molecular function
Biological process
Cellular component
Other terms are related to parent terms by inheritance relations (part of, IsA).
Genes assigned to terms by expert curators

8. List of Genes
List of Terms

9. Measuring GO term enrichment
Some GO terms are more common than others.
The more-common GO terms will occur by chance.
Key question: is a term more common in a gene list than expected?

10. Cytoscape BiNGO plugin
Estimates P value reflecting enrichment of each GO term.
Draws a graph of part of GO showing the enriched terms.

11. In this section, you will learn
Loading GO annotation data in Cytoscape with the OBO format.
Browsing through nodes by GO terms
Measuring significantly-enriched processes with BiNGO.