Comparison of Top MINE and MODE Cluster Results. Representative examples of cluster results from MCODE and MINE for the C. elegans interactome from WI8, showing the 14 highest-scoring clusters from each algorithm. For each method, parameters were chosen to provide the optimal balance between modularity and highest geometric accuracy for GO Cellular Component. Cluster size (n), local modularity (m), and density (d) are provided below each cluster. A) MCODE (vwp = 0.30; haircut = true). B) MINE (vwp = 0.90; mod = 0.30; trim = true).