I have collections of probe/genes from 3 different conditions (e.g. stimulated by chemical1 2 3). They are already selected based on some fold change threshold. What I want to do now is to look at GO that are preferentially occur in each of the above conditions.
I face two following ways to do it, which I'm not sure which one is the correct one to do:
Obtain GO for each of the conditions together with the p-value of the GO term. Then perform clustering (hierarchical/knn) on these p-values.
Perform the clustering for the foldchange or the expression values. Then for each of the clusters determine the GO.
Your advices would be truly appreciated.