About Fatigo+ Input Format

Question

[Dejian]

I have a list of genes with GO annotations. I want to see which GO categories are enriched. The list of GO identifiers were inputted into FatiGO+. However, five hours has passed and I did not get any results. The list of genes contains about 840 GO identifiers. Why does it take such a long time to compute? Is GO identifier a valid Ensembl identifier as stated in "Input format" at http://babelomics2.bioinfo.cipf.es/fatigoplus/cgi-bin/fatigoplus-help?

http://babelomics2.bioinfo.cipf.es/fatigoplus/cgi-bin/fatigoplus.cgi

Answer 1

[Lars Juhl Jensen]

Judging from your question and your comment to Jorge's answer, I think you have misunderstood what FatiGO does. Quoting the abstract, FatiGO is a tool "to extract Gene Ontology (GO) terms that are significantly over- or under-represented in sets of genes". The starting point is thus a set of genes, not a set of Gene Ontology terms.

It might be a good idea if you post a new question in which you describe what it is you are trying to achieve, because it looks to me as if you are trying to use FatiGO for something that it cannot do.

[Jorge Amigo]

I think this is exactly the point ;)

[Dejian]

Thank you, Lars and Jorge. I think you are right. The starting point is genes, not GO IDs. I will try other input formats. :)

Answer 2

[Jorge Amigo]

I didn't know that FatiGO accepted GO identifiers, so I went to the help file to confirm it. I only found on the input formats section that it accepts "HGNC symbol, EMBL acc, UniProt/Swiss-Prot, UniProtKB/TrEMBL, Ensembl IDs, RefSeq, EntrezGene, Affymetrix, Agilent, PDB, Protein Id, IPI...", but no GO identifiers directly. moreover, if you read carefully you will see that "These identifiers must be annotated in Ensembl and any gene not annotated in Ensembl will be lost in the analysis.". if you want to make sure that you are dealing with the appropriate identifiers I would suggest building a very simple BioMart query with them just to retrieve their gene names, and you will see if they are present or not on Ensembl.

once you have that sorted out, waiting for the results is all you can do. FatiGO is a reputated and well stablished tool that is build onto a large cluster broadly accessed, so maybe if you selected many checkboxes on the functional annotation section you may probably have to wait longer for the results.

[Dejian]

Thank you, Jorge. I noticed the mentioned formats in the help file. I am just thinking that FatiGO is designed to "find significant associations of Gene Ontology terms",so it should accept GO identifiers. Thirty hours have passed, I haven't received the results. I selected all possible checkboxes. Maybe this is why I haven't got the results.