Analysis

AmiGO Term Enrichment

Applies to:  Sequence Collection

Description

This analysis contacts the AmiGO server at http://amigo.geneontology.org/rte to perform gene ontology term enrichment analysis on a selected collection of sequences. Note that the AmiGO service relies on its own GO annotation database and does not use the GO annotations associated with the sequences in MotifLab. Therefore, in order to correctly determine the GO terms for each sequence, the sequences must originate from an organism supported by AmiGO and their names must be in a gene ID format recognized by AmiGO.

For more information, see the official documentation at http://geneontology.org/page/go-enrichment-analysis.

Arguments

NameDescription
Target set The set of sequences to analyse. This set can be specified either with a Sequence Collection (in which case AmiGO will use the names of the sequences as gene identifiers) or the list of gene identifiers can be supplied explicitly using a Text Variable.
Species The species that the sequences originate from
Ontology The ontology domain to use in the analysis. Three different options are available: Biological Process, Molecular Function and Cellular Component
Significance threshold A p-value threshold used by MotifLab to tag GO terms that score below this threshold as significant. Significant GO terms may be highlighted when output, for example by displaying them in a different color

See Also: Sequence Collection