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GSEA_Analysis

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dxjasmine edited this page Mar 10, 2020 · 6 revisions

Objective

  • Time estimated: 60 mins;
  • taken 60 mins;
  • date started: 2020-03-10;
  • date completed: 2020-03-10

Procedure

  1. Go to GSEA Homework
  2. Lecture 7 review and literature review
  3. Download mesenchymal vs immuno rank file
    • Genes are ranked by score and higher score shows that the gene is more expressed in the mesenchymal tissue
  4. Download genesets
    • version:February_01_2020
    • navigate to Human/symbol/Human_GOBP_AllPathways_no_GO_iea_February_01_2020_symbol.gmt
    • annotation: GO biological process, no IEA and pathways
  5. go to GSEA
  6. go to RunGESAPrerank，select mesenchymal vs immuno rank file as ranked file and Human_GOBP_AllPathways dataset as my gene sets; select no collapse; set max siz = 200; set min = 15. leave the rest as default
  7. result file is in out folder -- "index.html"

Results and Interpretation

  1. Explain the reasons for using each of the above parameters
    • gene sets database: mesenchymal-immunoreactive rank file as it
    • permutations: set permutation to 1000 which is large to generate a reasonable estimation.
    • ranked list: use mesenchymal-immunoreactive rank file as GSEA is trying to find gene sets that are enriched in mesenchymal or immunoreactive subtypes
    • collapse: no collapse as no need for collapsing
    • limit: set max to 200 in order to exclude extremely large datasets in some pathways
  2. What is the top gene set returned for the Mesenchymal subtype? What is the top gene set returned for the Immunoreactive subtype?

    • Top gene set for Mesenchymal subtype :

      • HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION%MSIGDB_C2%HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION
      • Enrichment Score (ES)= 0.86477077
      • Normalized Enrichment Score (NES) = 2.6065168

    • Top gene set for Immunoreactive subtype:

      • HALLMARK_INTERFERON_ALPHA_RESPONSE%MSIGDB_C2%HALLMARK_INTERFERON_ALPHA_RESPONSE
      • Enrichment Score (ES)= -0.8591
      • Normalized Enrichment Score (NES) = -3.0393002

Reference

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., … Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15545–15550. https://doi.org/10.1073/pnas.0506580102

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