Homework: GSEA - bcb420-2024/Dien_Nguyen GitHub Wiki

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

• The rank file contains the rankings of the genes, since we are running a pre-ranked GSEA analysis.
• We use the GO biological process with no IEA since they are more supported and provides more reliable results. GO:BP is also very well documented and is updated frequently.
• The default upper and lower limits for geneset sizes in GSEA are 500 and 15. By decreasing it, we decrease the computation time and possibly focus on more meaningful genesets.

Mesenchymal subtype

1. What is the top gene set returned for the Mesenchymal sub type?

• HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION%MSIGDB_C2%HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION

1. What is its pvalue, ES, NES and FDR associated with it?

• 0.0, 0.8635254, 2.5574074, 0.0

1. How many genes in its leading edge?

• 83 genes

1. • What is the top gene associated with this geneset?

• FBN1

Immunoreactive subtype

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

• HALLMARK_INTERFERON_ALPHA_RESPONSE%MSIGDB_C2%HALLMARK_INTERFERON_ALPHA_RESPONSE

1. What is its pvalue, ES, NES and FDR associated with it?

• 0.0, -0.85694104, -2.941609, 0.0

1. How many genes in its leading edge?

• 57 genes

1. • What is the top gene associated with this geneset?

• GBP4