Detect gene expression signatures in own dataset

Question

[SunRise2019]

I have a list of genes derived from RNA seq analysis, that according to a published paper are supposed build a certain signature

gene A
gene B
gene C
gene ..

I would like to test whether this signature exists in my gene-expression dataset, too.

What is the standard way of doing this? What R packages are to be recommended for this task.

I have screened the forum and google and couldn't find a satisfying explanation.

Thanks a lot.

[Arup Ghosh]

Please provide a link to the article you are talking about.

Answer 1

[vj]

If I understand correctly you have set of genes (G) and expression data (E), and you want to know if G is significantly enriched/depleted in E. If so, then you can use GSEA from Broad Institute. You have to somehow rank the genes in E (tpm,fpkm,log fold changes etc) and see if G significantly clusters at the top or bottom of this ranked E.