At present, the organization of system modules is typically limited to either a multilevel hierarchy that describes the vertical relationships between modules at different levels (e.g., module A at level two is included in module B at level one), or a single-level graph that represents the horizontal relationships among modules (e.g., genetic interactions between module A and module B). Both types of organizations fail to provide a broader and deeper view of the complex systems that arise from an integration of vertical and horizontal relationships.