We have characterized a type of cell that is different in its functions from other cells in general. We would like to create a gene signature from 4 samples that were sequenced with RNAseq.
I've been trying to learn a way to do this without comparing to other cell types, but if needed, this would be ok too.
Is there any literature or method that you guys recommend to creating a gene signature?
1 - We tought about finding the top expressed genes that have the least variance between samples, as one way. 2 - The other way was to find enriched pathways for the most expressed genes, select the pathways that are relevant to our biological condition and then apply the 1st filter (which risks losing relevant genes for the signature but keeps only genes relevant to both cell type and relevant biological pathway)
I've seen ssGSEA and other method but I don't understand how they can be usefull to find our own gene signature!
Is there any way to find the "similarity" between our 4 samples?
Any tips will be highly appreciated