Using the Gene Ontology (GO) Browser

This Gene Ontology (GO) Browser help document answers the following questions:

• How are Gene Ontology (GO) vocabularies structured?
• What can I use the Gene Ontology Browser to find?
• How do I browse the GO vocabularies?
• How do I search the GO vocabularies?
• How do I interpret the GO Browser Results?
• How do I interpret the Gene Ontology Annotations?

How are Gene Ontology (GO) vocabularies structured?

The Gene Ontology (GO) Consortium creates a controlled vocabulary of terms that describe the molecular functions, biological processes and cellular components of a gene's products. The GO vocabularies have a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. The range is useful for annotating genes and searching for gene information using these terms as search criteria. You can either browse or search the vocabularies. Organizing the ontology terms as a Directed Acyclic Graph (DAG), i.e., in which a term can have more than one parent, allows presentation of functions from multiple perspectives. The Gene Ontology uses three broad categories (Molecular Function, Biological Process, Cellular Component) to reflect the biological roles of genes:

Category	GO ID	Description	Example
Molecular Function	GO:0003674	Tasks performed by individual gene products.	Transcription factor; DNA helicase
Cellular Component	GO:0005575	Subcellular structures, locations, and macromolecular complexes	Nucleus; telomere; origin recognition complex
Biological Process	GO:0008150	Broad biological goals accomplished by ordered assemblies of molecular functions	Mitosis; purine metabolism

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What can I use the Gene Ontology Browser to find?

Use the Browser to find vocabulary terms that may be used to describe gene functions. You can choose a term or GO ID here to improve your searches with the Gene Ontology (GO) classifications field on the Genes and Markers Query Form as well as the appropriate fields on the Gene Expression Data Query and MGI Batch Query forms. Selected terms in the GO Tree View link to a listing of all genes annotated to the term and its descendants.

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How do I browse the GO vocabularies?

To browse the GO, click on one of the three broad categories beneath the page title (Molecular Function, Biological Process, Cellular Component) that reflect the biological roles of genes. In the GO Tree View, click on a term and navigate until you find the desired GO term. A black triangle at the beginning of a term indicates the term has subterms. Each selected term in the Tree View links to list of all genes annotated to the term. You can also click on Parent Terms in the GO Term Detail section to quickly move up the vocabulary hierarchy. You can expand branches by clicking on a term or its black triangle. If you click on a term, this also updates the GO Term Detail section. You can collapse branches by clicking on the downward-pointing triangle. Clicking on the triangles allows you to navigate the branches without updating the Term Detail section.

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How do I search the GO vocabularies?

To search the Gene Ontologies, enter any text string in the GO Search box:

• Begin typing a term of interest and an autocomplete list activates on the second character.
  • The list shows all the Gene Ontology terms and their synonyms that match your search characters.
  • When you enter a text string in the box, the GO Browser searches for all terms in all three categories (Molecular Function, Biological Process, Cellular Component) containing that string and any synonyms. For example, if you enter muscle, the Browser returns items which include muscle fiber development, muscle cell cellular homeostasis, and striated muscle contraction.
  • You can type the beginnings of multiple terms to narrow the list (example: oxid amin will limit the list to terms with oxidase AND amino).
• You must select a term. There is no free text searching in this field.
• You can only select one term.
• Enter an GO accession identifier in the Search field to return an exact match for the term.
• Use the return/enter key on your keyboard to activate a search. The search finds all GO terms that contain any of your search terms and displays a list of those terms.
• If you are uncertain which terms to use for the most effective searching, browse the ontology to see the standardized terms in the GO Tree View.

The first term listed in your search results is automatically selected and updates the GO Term Detail and GO Tree View sections on the right. Click on a different term in your search results to refresh the GO Term Detail and Tree View with the selected GO term. Use the Clear button to start a new search.

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How do I interpret the GO Browser Results?

GO Search	The search finds all GO terms that contain all of your search terms and displays a ranked list of those terms. Click on a term to update the GO Term Detail and Tree View sections of the page with the appropriate gene ontology terms and the selected term highlighted in blue.
GO Term Detail	Term The selected term is highlighted in blue. If you accessed this page by clicking on a term on another page, the appropriate GO term is highlighted. Otherwise, before you initiate a search or browse, the default term is the category term, Molecular Function. Synonyms Alternative search terms for the selected term Definition Official definition for the term Parent Terms The immediate parent terms for the selected GO term. Because the Gene Ontology is built on a DAG framework, a term may have more than one parent term. This means a term appears in multiple branches of the tree. For example, methylation is a metabolic process. The term has an "is a" relationship to the parent term. Comment Additional information about the use of this Gene Ontology term Category One of the three broad categories (Molecular Function, Biological Process, Cellular Component) used to reflect the biological roles of genes ID The unique accession ID for the Gene Ontology term Other IDs Alternative accession IDs for the Gene Ontology term
GO Tree View	The main category headings are shown beneath the section header. The number of genes/annotations to the selected term is shown. Child terms are shown beneath the selected term in the tree view. You can collapse or expand branches by clicking on a term. When you select a new term, it is highlighted in blue and the Term Detail section is updated. Click on the number of genes/annotations for a listing of all the genes annotated to the term.
"Is-a" Relationship	Indicates that the term is an instance or type of the more general term above it in the tree. For example, acetate ester metabolic process is a type of organic substance metabolic process.
"Part-of" Relationship	Indicates that the term is a component of the more general term above in the tree. For example, cell cycle arrest is a part of the cell cycle process.
"Regulates" Relationship	Indicates that the term modulates the frequency, rate, or extent of the term above it in the tree.
"Regulates upward" Relationship	Indicates that the term activates or increases the frequency, rate, or extent of the term above it in the tree.
"Regulates downward" Relationship	Indicates that the term stops, prevents, or reduces the frequency, rate, or extent of the term above it in the tree.
	A black triangle preceding a term in the Tree View indicates that the term has children. Click on the triangle to see the additional paths. You can collapse branches by clicking on the downward-pointing triangles. Unlike clicking on a term, clicking on a triangle does not update the selected term.
# genes,  # annotations	Number of markers annotated to the term and its descendants, followed by the number of annotations to each term and its descendants. Click this link to see a list of all the genes annotated to the term and its child terms.

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How do I interpret the Gene Ontology Annotations?

See: Interpreting the Gene Ontology Classifications Report

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