#5 Homework 2
Luka Trkla edited this page Apr 8, 2022
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2 revisions
| Start Date | End Date | Time Estimate | Time Taken |
| 2022 Mar 14 | 2022 Apr 8 | 1 Hour | 30 Min. |
- To familiarize oneself with G:Profiler for enrichment analysis purposes.
- Worked through the sample gene set provided in the assignment.
- What is the top term returned in each data source?
- GO biological process: immune system process GO:0002376 7.171×10-150
- Reactome: Immune System REAC:R-HSA-168256 6.800×10-78
- WikiPathways: TYROBP causal network in microglia WP:WP3945 1.161×10-20
- How many genes are in each of the above genesets returned?
- immune system process:2748 genes total
- immune system: 2041 genes total
- tyrobp:63 genes total
- How many genes from our query are found in the above genesets?
- immune system process:287 genes in query found
- immune system: 218 genes in query found
- tyrobp:27 genes in query found
- 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, many data points were removed; the top terms now have approx 130 genesets in GO:BP instead of the aforementioned 2748.
- Which of the 4 ovarian cancer expression subtypes do you think this list represents?
- Not 100% sure but almost every resulting term in the query deals with immune response, and online it says that immunoreactive is an expression subtype so I believe it would be of the immunoractive subclass.
- Going forward, I will practice using g:profiler.