amigo

Questions and answers that have to do with AmiGO specifically.

What are the differences between the data available in AmiGO and those on QuickGO?

These are some of the differences between EBI-GOA (QuickGO) and GO Central (AmiGO) when it comes to entities.

GO Central recommends that GAF annotations are made to genes, that is 1:1 equivalents. In GOA (and consequently in QuickGO) annotations are made to proteins, and there may be multiple proteins per gene, sometimes representing different isoforms. You will see this reflected in different numbers for mouse annotations for example.

How can I do term enrichment analysis for a species that is not present in the list from AmiGO?

The Term Enrichment tool on the GO and AmiGO websites center only on data from the genomes available on the PANTHER Classification System Database (http://go.pantherdb.org). Details about how to use the tools available on AmiGO and how to interpret the results is available on our website at http://geneontology.org/page/go-enrichment-analysis.

Where can I find the number of terms in each of the ontologies?

You can find the number of terms on each of the ontologies by going to AmiGO:

  • Under the 'Advanced Search' section in the middle of the page, use the drop-down menu to choose "Ontology". You don't need to type anything on the 'Quick search' box.
  • This action will send you to the 'Information about Ontology search' page. There, open the 'Ontology source' filter menu on the left. You will see that as of October-27-2015 the number of terms on per ontology were:

What is the best way to link into AmiGO?

AmiGO is under constant development and our suggestion is that you frequently check back for the most recent information (and code, accordingly). The most recent proposal for a stable API is available from the AmiGO 2 wiki manual.

What data does AmiGO use? Are there IEAs? If so, which ones?

AmiGO is reloaded approximately once a week. The files currently loaded into the public AmiGO instance can always be seen here.

AmiGO does currently load full Inferred from Electronic Annotations (IEAs) from UniProt, although this is in development. For a more full discussion of the data loaded into AmiGO, please see the FAQ.

How do I find manually annotated gene products only, i.e. how do I sort by evidence code?

Search results can be filtered using the filter menu on the left-hand side of the results page of an AmiGO search. Using the drop-down menu a variety of evidence codes or evidence code combinations can be added or removed to filter the set.

How do I install AmiGO locally?

Full documentation for downloading and installing AmiGO is available here .

How do I browse the GO?

The GO Consortium has developed AmiGO for searching and browsing the Gene Ontology and the gene products that member databases have annotated using GO terms. Entering a search term into the quick search menu and choosing an auto-completed choice from the drop-down will return the summary page for that gene product or term. Alternatively terms can be entered by free text and the user will be allowed to choose whether the search will return genes, terms or annotations.