Overview

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Overview

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

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Gene Ontology

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

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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

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List of Genes
List of Terms
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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?

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Cytoscape BiNGO plugin

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

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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.