Overview Gene Ontology Introduction Biological network data

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Presentation transcript:

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

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

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

List of Genes List of Terms

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?

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

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.