I'm interested in extrapolating what transcripts dictates differences between sample in a PCA from RNA-seq data. This is the PCA of RNA-seq on different samples (A,B,C,D,E,F,G):
Samples are in duplicate and are circled for better understanding. Bold samples are controls, samples connected with arrows are treated samples.
What I want to understand is what are the genes that "moves" A to B (Red Arrow) or A to C (Blue arrow). Given the partially similar trajectory of A to C and D to E the second question would be to check whether some genes in A to C are also responsible of the movement of D to E. This same comparison can be made from comparing A to B and F to G.
Do you happen to know a tool that can allow me to better address this questions?