Figure 2

SPIKE modeling scheme. State transition scheme vs. entity-relationship scheme. (A). The 'state transition' scheme regards different post-translational modified versions of a protein as separate entities (or as different 'states' of a protein), visually represents them as distinct nodes in the map, and aims at tracing the transition between these states. (B). In contrast, the 'entity-relationship' scheme views all these entities as one protein, and focuses on the regulatory effects between different proteins within a signaling network. In a state transition scheme, representation of signaling pathways could become extremely complex due to combinatorial growth of possible states. An entity-relationship scheme is much simpler, having all these states represented by only one entity, but at the price of not taking into account temporal order constraints on the state transition reactions in cases where such constraints exist.