Homework assignment - G:Profiler1.

List of genes: genelist.txt

Note: Had to Select the Ensembl ID with the most GO annotations (all)

1. What is the top term returned in each data source?

For GO:BP

• Term Name: immune response
• Term ID: GO:0006955
• Padj = 6.737 × 10^-149

For REAC

• Term Name: Immune System
• Term ID: REAC:R-HSA-168256
• Padj = 5.296×10-79

For WP

• Term Name: Allograft rejection
• Term ID: WP:WP2328
• Padj = 2.815×10-22

2. 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) For GO:BP: 2008 genes

For REAC: 2079 genes

For WP: 88 genes

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

For GO:BP: 431 genes

For REAC: 337 genes

For WP: 303 genes

4. 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?

Yes that changed the results:

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

I think either the mesenchymal or immunoreactive subtypes, due to the notable presence of genes involved in cell-matrix interactions and immune responses, respectively.

6. 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?

TFEC, corresponding to the gene ID ENSG00000105967, did not return any associated pathways based on the specific search parameters set in our query. A comprehensive search using all available terms yielded results only under the microRNA data source, specifically identifying two microRNAs: ebv-miR-BART7-3p and hsa-miR-506-5p, without any direct links to TFEC.