G:Profiler - bcb420-2024/Krutika_Joshi GitHub Wiki

What is the top term returned in each data source?

• In GO:BP, immune system response is returned.
• In KEGG, antigen processing and presentation is returned.
• In REAC, Immune system is returned
• Overall, it seems the immune response is the top term returned.

How many genes are in each of the above genesets returned? (hint, in the Detailed results tab of g:profiler results if you click on the arrows next to the stats heading you will be able to see the number of genes in a term, number of genes in your query and number of genes in your query that are also in your term)

• There are 2776 genes in the immune system response term in GO:BP.
• There are 69 genes in the antigen processing and presentation term in KEGG.
• There are 56 genes in the immune system response term in REAC.

How many genes from our query are found in the above genesets?

• There are 287 genes found in GO:BP.
• There are 69 genes found in KEGG.
• There are 56 genes found in REAC.

Change g:profiler settings so that you limit the size of the returned genesets. Make sure the returned genesets are between 5 and 200 genes in size. Did that change the results?

• KEGG and GO:BP still have immune response/antigen processing and presentation as the first term but REAC changed to degradation of DVL.

Which of the 4 ovarian cancer expression subtypes do you think this list represents?

• I would think this list represents the immunoreactive subtype as the immune response is the most observed term across all the data sets.

Bonus: The top gene returned for this comparison is TFEC (ensembl gene id:ENSG00000105967). Is it found annotated in any of the pathways returned by g:profiler for our query? What terms is it associated with it g:profiler?

• I doesn't seem to be annotated for any pathways as when I click on the "Detailed results" tab and checking for TFEC, it shows up as the first option but I don't see any colored boxes in any of the pathways.