7. GSEA - bcb420-2022/RuoXuan_Wang GitHub Wiki

Objective

Practise using GSEA

Duration

Time estimated: 1.5 h; taken 1.5 h;
date started: 2022-03-22; date completed: 2022-03-22

Progress

• Perform a GSEA preranked analysis with ranked list comparing mesenchymal and immunoreactive ovarian cancer subtypes (mesenchymal genes have positive scores, immunoreactive have negative scores)
• Use following parameters:
  • mesenchymal vs immuno rank file
  • genesets from the baderlab genesets 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

Answer questions:

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

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

3. 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

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• Record results in journal

Conclusion and outlook

• Assignment 3 due next

References