Gene Ontology GO Project

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Gene Ontology (GO) Project http//www.geneonto
logy.org/ Reference http//www.geneontology.org
/GO.teaching.resources.shtml
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• The GO project has developed three structured
  controlled vocabularies (ontologies) that
  describe gene products in terms of their
  associated biological processes, cellular
  components and molecular functions in a
  species-independent manner.

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GO browser
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GO structure

• GO terms divided into three parts
• cellular component
• molecular function
• biological process

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• Each entry in GO has a unique numerical
  identifier of the form GOnnnnnnn, and a term
  name, e.g. cell, fibroblast growth factor
  receptor binding or signal transduction
• Each term is also assigned to one of the three
  ontologies, molecular function, cellular
  component or biological process.

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Cellular component

• A cellular component is just that, a component of
  a cell, but with the proviso that it is part of
  some larger object this may be an anatomical
  structure (e.g. rough endoplasmic reticulum or
  nucleus) or a gene product group (e.g. ribosome,
  proteasome or a protein dimer).

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Cellular Component

• where a gene product acts

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Cellular Component
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Cellular Component

• Enzyme complexes in the component ontology refer
  to places, not activities.

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Molecular Function

• Molecular function describes activities, such as
  catalytic or binding activities, that occur at
  the molecular level.

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Molecular Function

• activities or jobs of a gene product

glucose-6-phosphate isomerase activity
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Molecular Function

• insulin binding
• insulin receptor activity

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Molecular Function

• A gene product may have several functions a
  function term refers to a reaction or activity,
  not a gene product
• Sets of functions make up a biological process

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Biological Process

• A biological process is series of events
  accomplished by one or more ordered assemblies of
  molecular functions. Examples of broad biological
  process terms are cellular physiological process
  or signal transduction.

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Biological Process

• a commonly recognized series of events

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Biological Process

• transcription

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Biological Process

• regulation of gluconeogenesis

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Ontology Structure

• Terms are linked by two relationships
• is-a ?
• part-of ?

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Ontology Structure
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GO structure

• GO isnt just a flat list of biological terms
• terms are related within a hierarchy

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GO structure
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GO structure

• This means genes can be grouped according to
  user-defined levels
• Allows broad overview of gene set or genome