Journal Entry #3: G:Profiler - bcb420-2023/Helena_Jovic GitHub Wiki
Objective
Time Management
Date Started: 2023-03-02
Data Completed: 2023-03-02
Estimated Time: 1.5 hours
Actual Time: 1 hour
Workflow
- Used this list of genes:genelist.txt as a query set and run a g:profiler enrichment analysis
- Used the following parameters: Data sources : Reactome, Go biologoical process, and Wiki pathways Multiple hypothesis testing - Benjamini hochberg
- Changed the term size to 250 under the Detailed Results tab
- Checked if TFEC is annotated to any of the returned pathways using search function.
Questions
- What is the top term returned in each data source?
Reactome: Immune system.
GO Biological Process: Immune system process.
Wiki Pathways: TYROBP causal network in microglia.
- 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)
Reactome: 2,041
GO Biological Process: 2,683 Wiki Pathways: 60
- How many genes from our query are found in the above genesets?
Reactome: 330
GO Biological Process: 426
Wiki Pathways: 289
- 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?
After changing the term size to be between 5 and 200, I noticed a significant difference in the results.
Top term in each data source: Reactome: Immunoregulatory interactions between a Lymphoid GO Biological Process: antigen processing and presentation Wiki Pathways: TYROBP causal network in microglia
Genes in each gene set:
Reactome: 181
GO Biological Process: 108
Wiki Pathways: 60
Genes in each query:
Reactome: 330
GO Biological Process: 426
Wiki Pathways: 289
- Which of the 4 ovarian cancer expression subtypes do you think this list represents?
Immunoreactive subtype, which is identified by the presence of immune cells in the tumor microenvironment and a robust immune response.
- 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?
No, it isn't found annotated in any of the pathways return by g:profiler for this query.