I'm investigation the role of my gene of interest (GOI) in two types of cancer.

Since it is a low expressed gene, it is not an important DEG. If I run edgeR, I don't find it, using FDR < 0.5.

I decided, then, to run gene co-expression analyses using CEMiTool (www.bioconductor.org/packages/release/bioc/html/CEMiTool.html).

Using this strategy, I detected modules (one for each kind of cancer) containing my GOI and co-expressed genes.

Now I want to run pathways analyses, to discover the pathways associated with these modules. I'm trying to use fgsea (bioconductor.org/packages/release/bioc/html/fgsea.html), but fgsea asks me to rank the genes in each module by p-value. That works for DEGs that are normally listed by FDR and p-value, but CEMiToll gives me only the list of genes that are correlated with my GOI, it doesn't give me a value to rank them.

How can I investigate the pathways associated with these modules, if I only have the genes names?

If I put these genes on EnrichR (maayanlab.cloud/Enrichr/), I can detect the pathways and have all the results I want, but I would like to do these analyses using the command line. How is EnrichR performing these analyses without a rank list? How can I reproduce the analyses performed by EnrichR using the command line and the Reactome database? Is there a package in R for that?



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