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
- Open pantherdb.org on your browser and select a file or copy and paste your data into the text box in step #1
- Select an organism for step #2
- Select statistical over-representation test for step #3 and de-select the 'use default settings' checkbox.
- 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.
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:
- g:Profiler (http://biit.cs.ut.ee/gprofiler/)
- Just Annotate My Proteins: Info available at http://jamps.sourceforge.net/ Download available from https://github.com/genomecuration/JAMp
- Ontologizer (http://compbio.charite.de/contao/index.php/ontologizer2.html): you can use any annotation file. If available for your species of interest, use the complete UniProt association file, gene_association.goa_uniprot.gz, available at ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/ However, if you have questions about how to use this tool, you would need to contact the Ontologizer developers directly as this is not maintained by the GO Consortium.
- blast2go https://www.blast2go.com/ – but beware, many of the annotations propagated may be incorrect, depending in part on the phylogenetic distance to the nearest well-annotated genome.