Scheme of the ProtoNet hierarchy test. (A) The ProtoNet binary tree. Vertices in the graph are protein clusters. Crossed-out vertices are eliminated because they do not match any GO term. (B) Tree hierarchy of remaining ProtoNet clusters. Remaining nodes correspond to GO terms. (C) The corresponding GO DAG hierarchy between the vertices. (D) Intersection of graphs in B and C shows the amount of hierarchical correspondence between GO and ProtoNet. In this example, there are 6 edges common to GO and ProtoNet. 2 of the ProtoNet edges do not appear in GO and 4 GO edges do not appear in ProtoNet.