I’m pretty new to computational biology and to transcriptomics. I’m currently trying to characterize how the overexpression of three transcription factors (x, y, z) acts on the transcriptome of a cell line.
The design involves 5 groups of samples (x, y, z, xyz, Ctrl), each group containing 5 replicates. Data has been filtered for 0 counts removal.
As far as I've noticed each of the TFs induces or represses some genes, as highlighted by differential gene expression analysis performed using DESeq2 (using the Ctrl condition as reference). I’ve runt PCA analysis using FactoMineR on all the expressed genes, with count values transformed as regularized log as suggested in DESeq2 pipeline. Plotting the samples over the first three PC, I’ve noticed something pretty curious.
Basically it appears as each TFs (x, y, z) is “pulling” the Ctrl state along a certain “dragging” path, while the path related to the simultaneous overexpression (xyz) seems to be the sum of the three (x+y+z) actions. I’m wondering whether any of you can suggest any method to test this hypothesis.
Thanks in advance for any suggestion.