Hi there,
I seem to be unable to do any specific functional enrichment analyses whenever I upload a background universe in addition to my protein lists.
For reference, I tried uploading a .csv or .txt file containing Uniprot IDs as a background universe. The background universe Uniprot IDs are mapping fine. The background universe ranges from 600-11,000 proteins and my proteins of interest range from 48-4,900. I am able to select Generic PPI and any of the build and database options ok. I also get a network of proteins. It’s only when I try and do anything in the function explorer (e.g. GO BP, Reactome, KEGG, etc.) that I get the error: “Failed to perform enrichment test! It cannot be used for user uploaded networks”. If I do not use a background universe, I have no problems using the function explorer.
Am I doing something wrong or is this a known issue? Are there any workarounds you can suggest so that I can set a background universe for my enrichments?
Many thanks for your help!