I'm working on a project to find out the key characteristics of different cell subclones derived from a heterogeneous cell population, based on their RNA-seq gene expression profile. So for example, clone A is known to have immune-functions and I wanted to find out if clone B shares similar characteristics with clone B. I screen out the differentially expressed genes in B compared to A and did KEGG pathway enrichment analysis on both up- and down-regulated DEGs respectively.
The results I got were that up-regulated DEGs in B were enriched in immune-related pathways, but some of the KEGG pathways were enriched by both up- and down-regulated DEGs. So I'm just wondering if I'm right to make the following interpretations: 1. the KEGG pathway analysis of up-regulated DEGs in B showed some of the main characteristics of B, and therefore B might also have immune-related functions (as these genes were up-regulated in B compared to A, and that they were related to immune pathways, so I thought this points that B is also immune-related) 2. the pathways that were enriched by both up- and down-regulated DEGs might be some common characteristics between A and B (as I assumed down-regulated in B= more highly expressed in A, and therefore pathways enriched by down-regulated DEGs might show characteristics of A, and pathways enriched by both up and down= common between A and B?)
I am totally new in this field and this is my first time doing this sort of analysis and interpretation, so some of what I said might be totally nonsense. I would really appreciate any comments and thank you!