For each perturbagen member of a candidate class, we assessed whether it sufficiently recovered its expected connections to other perturbagens in at least one cell line via ROC analysis (more detail below). The class definition was refined to include only those members that passed this criterion. Finally, the classes were assessed for sufficient interconnectivity. We required that classes had at least 3 members and exhibited a median pairwise τ of at least 80 in one or more cell lines. Those classes that passed this filter were codified into perturbagen classes (PCLs). This process resulted in 171 PCLs (92 compound, 60 LoF, and 17 GoF classes) corresponding to 930 unique perturbagens. PCLs range in size from 3 to 44 members, with an average size of 5.8 members. PCLs were required to contain only perturbagens of the same type and although perturbagens were allowed to belong to more than one PCL, most PCLs are completely distinct, with a median pairwise overlap of zero members. 95% of PCL members belong to just one PCL.
