single gene GSEA
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4 weeks ago
asalimih ▴ 30

I have a candidate gene which I want to check if it is related to important pathways/gene-sets in a dataset that its samples are from one biological group (tumor samples). I came up with two methods:

  1. Projecting the expression matrix to gene-set space using ssGSEAProjection and then getting the correlation between my candidate gene expression and enrichment scores.
  2. Grouping samples into low and high expression groups based on the candidate gene and running a standard GSEA.

are these approaches correct? or is there any other method to do this properly?

To give more context, I chose this candidate from another dataset which had normal and tumor samples (using DEA and GSEA)

ssgsea gsea • 105 views

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