I have recently started working on a substance's effect on a cell line in different dosages. for this, there is a tool called bmdexpress2 that I am using. its input is the normalized counts from RNASeq for each dosage as a big matrix. when it comes to pathway analysis step, unlike hallmarks of GSEA, this tool uses some databases for defining pathways which involve pathways of even 2-3 genes.
So what I want to discuss here is the strength of small pathways and filtering thresholds. How can we bioinformatically decide on the importance of a pathway made of 3 genes? Should we just filter them out as there are much more comprehensive pathways? Or their GO Levels matter? Also there are many cases that out of those 3 genes, 1 of them is differentially expressed; is having 1 gene diff. expressed out of X genes in a pathway is enough to say that the pathway is enriched?
Here is an example go term for a small pathway.