7. GSEA Homework: HW 3 - bcb420-2022/Inika_Prasad GitHub Wiki

Given the ranked list comparing mesenchymal and immunoreactive ovarian cancer subtypes(mesenchymal genes have positive scores, immunoreactive have negative scores). Perform a GSEA preranked analysis using the following parameters:

  • mesenchymal vs immuno rank file (Links to an external site.)
  • genesets from the baderlab geneset (Links to an external site.) collection from March 1, 2021 containing GO biological process, no IEA and pathways.
  • maximum geneset size of 200
  • minimum geneset size of 15
  • gene set permutation

  1. Explain the reasons for using each of the above parameters.

  2. What is the top gene set returned for the Mesenchymal subtype?

  3. What is the top gene set returned for the Immunoreactive subtype?

For each of the genesets answer the below questions:

  1. What is its pvalue, ES, NES and FDR associated with it.
  2. How many genes in its leading edge?
  3. What is the top gene associated with this geneset.