Run GSEA with custom gene sets?

Question

[O.rka]

Is there a way to use custom gene sets using GSEA? I downloaded GSEApy and would love to use it within Python but if this is not possible then I can definitely use the commandline version.

For example, what if I had the following data:

# Gene list
gene_list = [
"gene_A", 
"gene_B", 
...
"gene_xyz"
]

and then a bunch of gene sets like this:

gene_sets = {
"gene_set_1": ["gene_A", "gene_B", ...],
"gene_set_2":["gene_B", gene_C", ...], 
...
"gene_set_100":["gene_A", "gene_T", ...]
}

I also have expression data for all of this with multiple samples if that could be used as well.

Is there still a way to run GSEA(py?) to figure out which gene sets are enriched?

I usually deal with microbiome datasets with de-novo called ORFs from prodigal so there are no gene ids that would be useable. A lot of my friends in cancer labs always talk about GSEA but I don't have the types of IDs that they use. Though, I still have "gene sets" that I could use so I feel like it could still apply.

Answer 1

[h.mon]

For the command-line, you have to prepare the gene-set in gmt format, and pass it with -g gene_sets.gmt. For the API, you have to use the gene_sets parameter from the gseapy.gsea() function.