guilt by association
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6 days ago

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.

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, 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, 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?

pathways analyses R • 228 views
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So fgsea is essentially the R version of GSEA. Its ranked based, that means that you cannot subset a set of genes. What you could do is more a of hypergeomtric test instead; which means that you take the list of genes and run the analysis, for R I think limma has an equivalent or just plug into something like cluego, david or panther.

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"fgsea asks me to rank the genes in each module by p-value." P-value of what?

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edgeR compares the counts of the cancer samples versus controls and gives the results (DEGs) in order, by fold change...with p-values and FDRs.. in fact, I believe the most appropriate is to select a FDR and rank the results below this FDR by logFC..

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Entering edit mode
6 days ago
Hyper_Odin ▴ 90

https://cran.r-project.org/web/packages/enrichR/index.html

Please refer to the paper for detailed explanation about analysis https://pubmed.ncbi.nlm.nih.gov/27141961/

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