View source for AmiGO Manual: Term Associations

=Overview=

The Term Associations page displays the gene products that have been annotated to that GO term and its children terms. This page is accessible from the '''View Associations''' hyperlink in the [[AmiGO_Manual:_Term_Search | term search results]] or from the '''Term Associations''' hyperlink on a [[ AmiGO_Manual:_Term_Details | GO term details page]]. The data can be downloaded in RDF-XML format.

=Annotation Table=

Since the Term Associations page can display all gene products annotated to a GO term and its children GO terms, the gene products displayed are organized by GO term. The GO term of interest is listed as the heading of the section and all gene products that have been annotated to that GO term are listed below.

[[Image:Ta2.png]]

Each gene product will have the following information associated with the annotations:

==Qualifier==

The Qualifier column is used for flags that modify the interpretation of an annotation. Allowable values are ''NOT'', ''contributes_to'', and ''colocalizes_with''. See the [http://www.geneontology.org/GO.annotation.shtml#qual GO annotation guide] for more information. 

==Name / Symbol==

Clicking on a gene product name brings you to the [[AmiGO_Manual:_Gene_Product_Details | gene product details page]] for that gene product. If the gene or gene product has a sequence available, there is a BLAST link, which, when followed, will submit the gene product to the [[AmiGO_Manual:_BLAST | AmiGO BLAST server]]. 

==Information==

The type of gene product (gene or protein) and the species from which it comes 

==Evidence==

Every GO annotation (or term association) must indicate the type of evidence that supports it; these evidence codes correspond to broad categories of experimental or other support. Mouse over the evidence code to see the full name of an evidence code. Clicking the selected evidence code will display the [http://www.geneontology.org/GO.evidence.shtml evidence code documentation page] where detailed description of the selected evidence code can be found. 

==Reference==

Clicking the reference hyperlink will display the reference used to make the association. 

==Assigned by==
The database or group that made the annotation is listed. If this is different to the database from which the gene or gene product comes, it will state that the data were submitted "via" another data source. 

Further detail about the information associated with an annotation can be viewed in the [http://www.geneontology.org/GO.annotation.shtml#fields Annotation File format documentation].

The checkbox on the left of each row of the table can be used to download the FASTA sequence for one or more proteins, or to get an [[AmiGO_Manual:_Gene_Product_Annotations | overview of the annotations]] to a set of gene products. Select the gene products you are interested in, pick the appropriate option using the radio buttons at the bottom of the page, and hit '''Submit Query''' to view the results.

Since a GO term can have multiple child terms and many gene products can be annotated to each GO term, the results pages may be paginated.

=Filtering=

Term associations can be filtered by the species and by the database from which the gene product comes, and the evidence code(s) of the association.

The type of associations shown can also be specified. '''All associations''' will display gene products annotated to the GO term or to any of its children; '''direct associations''' will display only gene products annotated directly to the term.

Multiple options can be selected in the species, data source and evidence code 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 associations.


[[Category:AmiGO_Manual]]
[[Category:AmiGO]]