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.

Below we have listed a few alternatives for organisms not included in the data available from the PANTHER Classification System Database:

  • If your organism of interest is not listed on the PANTHER data, you can still use the enrichment analysis tool available at PANTHER to do enrichment on proteins from your organism of interest, but you need to do some preparatory work beforehand. This paper tells you how to prepare input file for organisms not included in the PANTHER set. http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.092.html
    1. Open pantherdb.org on your browser and select a file or copy and paste your data into the text box in step #1
    2. Select an organism for step #2
    3. Select statistical over-representation test for step #3 and de-select the 'use default settings' checkbox.
    4. The system will prompt with a selection summary page. There is a 'change' button for reference list. You can press this button and update the reference list. You can either choose a different organism or upload your own reference list.
  • InterProScan: You may also annotate the coding sequences from your transcripts using the tools from InterProScan. This can be done either using WebServices or by downloading the tool and running it locally. Details are available at: http://www.ebi.ac.uk/interpro/search/sequence-search This will predict GO terms based on domains detected using the mapping file available from: http://geneontology.org/page/download-mapping At this time this will give you a relatively high level set of GO annotations, but we are working with the InterPro group to incorporate PANTHER families and detailed GO annotations on Panther trees.

Alternatively, you may also try conducting term enrichment analyses using a third-party tool, that is, one not maintained by the GO Consortium. We have listed a few of them below: