Network Miner also studies the role of the list MCN as a unit of action within the interactome. In particular, Network Miner tests four topological parameters:

1. Node connections degree, which was computed as the number of edges (interaction events) for a node
2. Betweenness, which depends on the number of shortest pathways passing through a given node
3. Clustering coefficient, which measures the connectivity of the neighbourhood
4. Number of components of the network

The three first parameters (degree, betweenness and clustering coefficient) are calculated for all the nodes in the MCN. Thus, a distribution of values for any of these parameters can be derived for each particular network. The comparison of two MCNs by contrasting how different they are in terms of their characteristic parameters is straightforward by a Kolmogorov–Smirnov test.