AmiGO Manual: Browse

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The AmiGO term browser allows you to view and navigate the terms in the Gene Ontology.

Tree View

AmiGO presents the ontology as a tree structure; this view is available from the Browse link in the menu bar on each page, and in the Term Lineage section of the term details page.

An example of part of the GO tree under biological process is displayed below:

Tb5.png

The tree structure holds information about GO terms and the relationships between them. Indentation is used to represent term parentage, with more specific terms - known as child terms or subclasses - being indented with respect to their parent terms. Terms with the same level of indentation are referred to as siblings.

Each line in the tree view contains the GO ID and the GO term name; clicking on the ID or name will open the Term Details page, containing more information about the GO term.

Term lines in detail

Let's use the following line as an example:

Tb6.png

The first icon on each line represents information about the children of the GO term. A open icon means that the term has child term(s) which are not shown in the current view; to view the children, click the open icon.

A close icon means that the term has been selected and all of its children are shown in the tree (as pigmentation is in the tree shown above). The node can be collapsed, hiding the children of the term, by clicking the close icon.

The leaf node icon means that the term is a leaf node which does not have children.

The second icon represents the relationship of the term to its parent term. GO uses several relationships: is_a (represented by Icon-is a.gif), part_of (represented by Icon-part of.gif), develops_from (represented by Icon-develops from.gif), regulates (represented by Icon-regulates.gif), positively_regulates (represented by Icon-positively regualtes.gif), and negatively_regulates (represented by Icon-negatively regulates.gif).

The GO ID and the GO term name are followed by two additional pieces of information.

The number in brackets after the term name represents the number of genes and gene products that have been annotated to that GO term and its children. Clicking on the number will take you to a full list of the genes and gene products that have been annotated to that GO term and its children.

If you have any filters active, the number displayed may change to reflect the filter. For example, selecting a filter to only look at genes or gene products from FlyBase will lower the number. For the evidence code and species filters, the numbers of genes associated to a term cannot be easily computed and AmiGO does not show a number.

If a GO term is fully expanded (i.e. all its children GO terms are displayed), a bar chart icon will appear at the end of the line. Clicking on this icon will generate a bar chart showing the distribution of genes and gene products associated with that GO term and its children.

Viewing Options

The links box gives users to view or save the tree they have created. Graphical View shows the tree as a graph using the GraphViz plug in, and users can then download a GraphViz dot file; Permalink provides a stable link to the tree. The tree can also be downloaded as GO RDF-XML or GO flat file format.

Filtering

The tree can be filtered by ontology to limit the display to the selected ontology or ontologies; the default is to display all ontologies.

The gene product counts displayed next to each term can be filtered to show the number of gene products from the selected data source(s). At present, evidence code and species filters are not available as the association count is difficult to calculate, and if you currently have these filters set, an additional checkbox will appear, allowing you to reset them.

Multiple options can be selected in both ontology and data source filters; select more than one option by control-clicking (apple-click on a Mac) the names. Click Set filters to set your display options. If no options are selected or you click Remove all filters, AmiGO will display all ontologies with full association counts.