GO terms : Ensembl ID / enrichment analysis

Question

[Sarah]

Hi

I have two lists of human genes.

I used FatiGO for enrichment analysis

FatiGO takes two lists of genes and convert them into two lists of GO terms using the corresponding gene-GO association table.

My gene identifier is a Ensembl Gene identifier (ENSG...). I obtain some results but I don't understand how does it occurs. Indeed, my Ensembl Gene identifier are not present in the http://geneontology.org/gene-associations/gene_association.goa_human.gz table (only Ensembl:ENSMUSP and Ensembl:ENSRNOP are present), so how FatiGO make the conversion?

• A gene can be associated to multiple GO Terms. We don't obtain the information concerning all the GO terms associated to each of the gene and how these GO terms are distributed among the three ontologies.

Is it possible to obtain this information?

Is it possible to obtain the file corresponding to the GOSlim GOA human database?

Thanks in advance

Answer 1

[Emily]

The ENSP/ENS###P IDs are protein IDs, whereas your ENSG/ENS###G IDs are gene IDs. GO terms are associated with proteins, not genes and genes may have multiple protein products. If you feed the tool with gene IDs, it will convert them into the corresponding protein ID(s) and get the GO terms for each of them. If you want to convert between gene and protein IDs, you can do so easily (and get GO terms) using BioMart. There's a help video here to get you started.

[lkmklsmn]

I thought the "gene"-ontology associates genes (not proteins) with terms...

[Sarah]

Hi

Thanks for your response Emily_Ensembl.

Yes, GO terms are associated with proteins. So now, I give Ensembl Protein identifiers (ENSP...) to FatiGO.

Here is the differents gene-GO association tables (ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/) provided by the consortium (Uniprot-GOA project). None of these tables contains Ensembl Protein identifiers corresponding to human (i.e ENSP), only Ensembl Protein identifier corresponding to mouse (ENSMUSP) and ratus (ENSRNOP) are present. So how FatiGO makes the conversion? In other words, which gene-GO association table is used?

I just find this file ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz, is it the file used?