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 contains 5 replicates. Data has been filtered for 0 counts removal.
Each of the TF induces and represses some genes (differential gene expression analysis has been carried using DESeq2, using the Ctrl condition as reference). I’ve runt PCA analysis on all the expressed genes (count values transformed as regularized log as in DESeq2 pipeline) using FactoMineR. 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.