This is a bit of a shot in the dark, but here goes nothing:
I have RNAseq from a cancer cell line. Control vs 2 treatments. Two timepoints at 12 and 48h. I have already run the standard pipeline of DESeq2 and enrichment of GO terms.
|#DEG||down 12h||up 12h||down 48h||up 48h|
The analysis shows a significant enrichment of Cell Death in upregulated DEG and of Cell Division among downregulated DEG (in both treatments, and at both timepoints).
When comparing the two timepoints within a treatment, Cell Division is enriched among downregulated DEG, and there is no enrichment for Cell death. I also detect some small differences when comparing treatment A vs treatment B.
I have already been able to get an idea of the dynamics of each of the Biological Process separately. However, I don't know of any way to compare the "magnitude" of each of the two almost-mutually-exclusive processes going on within each sample.
I basically want to measure "how many cells are dying" vs "how many cells evaded death/treatment and are dividing again". Is that possible?
Is there any way where, using only this bulk RNAseq data, I can infer which fraction of the cells within each sample are dying / repairing / dividing?