I have a basic question about RNAseq normalisation while comparing cancer/tumor tissue expression data to normal tissue expression.
Assuming that cancer cells will be highly proliferating, most of the cells are in S/G2/M phase whereas normal cells will be more in G1 phase. Hence if we are comparing a gene which is expressed during S-phase, it will show that tumor cells have high expression tumors, whereas if we are comparing a gene which is suppressed during S/G2/M it will be highly expressed in normal cells. How this is accounted for in RNA-seq analysis?
For example, I want to know a specific pathway and/or expression of a gene is expressed highly in tumor cell lines because of aberrant activation of pathway/gene or just because of the predominance of the specific phase of cell cycle, although in many cases both mean the same.