AmiGO Manual: RG Details

Overview

The Reference Genome details page is a detailed display of all GO information for a particular gene family (homolog set). For more information about the reference Genome project, please see the documentation.

The available information if broken into an Information section and a Summary for ... section.

Information

Visualizations

A visual version of the information on this page is available through the static and interactive links. The static version is mostly self-explanatory, but the interactive version is a little bit more nuanced; more detailed information can be found about it on its page in the manual.

Key

IDA, IGI, etc. (experimental) label

Indicates that there is at least one annotation to the term with direct experimental evidence by the labeled evidence code. There may be other non-experimental annotations as well.

ISS label

Indicates that there are no annotations based on direct experimental data, and at least one annotation by sequence similarity (ISS). There may be other non-experimental and non-ISS annotations as well.

text-only label

Indicates that there is an annotation to a term, but the evidence is neither experimental nor ISS or one of its sub-classes. Typically TAS or NAS.

bold entry

Indicates a direct annotation.

(blank) entry

Indicates that there is currently no homolog for that species at that term.

Jump to

You may jump directly to the terms for a particular ontology using these links.

Order terms by

In addition to the default order, you may also view the terms in a couple of additional orders.

• depth: order by the maximum depth of the go term in the graph.
• information content: the amount of "surprise" for seeing an annotation to that term. This is discussed in more detail in the OBD documentation under Information Content Metrics.
• name: order alphabetically.

The default is information content.

Summary for ...

The left-most column of this section is a list of GO terms that have been annotated with a gene product that has been identified as a homology for this page's gene family. This includes transitive annotations.

All of the other columns are species columns ans contain information of that species' annotations to the term in question. If a column's header (the species' name) is colored, the there is at least one annotation for that species in that ontology. An annotation will be represented by a gene product name and a label indicating the best evidence available for that annotation ( see above).