AmiGO Manual: Gene Product Search

Simple Gene Product Search

The gene product search is available from the AmiGO home page or by clicking on the Search link in the toolbar at the top of all pages in AmiGO. Enter one or more words into the query box and select the gene or protein name radio button. AmiGO will search gene product names, symbols and synonyms, and will return any gene products that contain the query word or phrase.

If you know the name or symbol of the gene product you are looking for, select the exact match checkbox to return only gene products which fully match your query.

Searching additional fields

By default, the gene product search looks at gene product names, symbols and synonyms. To search by sequence accession or by database ID, please use the Advanced Search option in the toolbar at the top of the page.

Search results

The results table lists the gene product(s) that match the query, with the part(s) of the gene product name that match the search term(s) highlighted in green. If the query match is in the gene product synonym(s), the matching synonym(s) will be displayed below the gene product name. If there is more than one matching synonym, the first synonym will be shown, followed by the text and x more; clicking on this text will display all the matching synonyms.

Clicking on a gene product name brings you to the 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 BLAST server. The right column of the table provides brief information about the type and species of origin of the gene product.

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 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.

Filtering

Gene product searches can be filtered by the species and by the database from which the gene product comes. You can also filter gene products by their associations, limiting the gene products shown to those which are annotated to terms in the selected ontology (or ontologies) with the chosen evidence code(s).

Multiple options can be selected in all the 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.