Suppose there is a data set which records protein information at time point 1 and 2. At time point 1, all subjects protein information are recorded. Right after time point 1, some subjects receive treatment or placebo. Then at time point 2, subject protein information are recorded again. For individual time point 1 and 2, I can perform over representation analysis at each time point. However, I do not know how to compare whether the treatment significantly affect pathways.
How do I compare pathways over representation analysis affected by treatment? I would like to conclude some pathways are inhibited or promoted by treatment.