Table 1 Description of subnetwork detection methods
Method name | Algorithm | Tool type | Input |
|---|---|---|---|
jAM_SA | Simulated annealing | Java;Cytoscape | PPI and p-values |
jAM_GS | Greedy search | Java;Cytoscape | PPI and p-values |
BioNet | integer-Linear Programming | R package | PPI and p-values |
BMRF | Greedy search | Matlab | Gene expression matrix, PPI, label and seed genes |
FEM | spin-glass algorithm | R package | PPI and t statistics |
Cosine | Genetic algorithm | R package | Gene expression matrix and PPI |
ClustEx | Clustering,shortest path | C | PPI and seed genes |
WMAXC | Continuous genetic algorithm and a projection procedure | Matlab | Gene expression matrix and PPI |
PinnacleZ | Greedy search | Java;Cytoscape | Gene expression matrix, PPI and label |
KR | Klein-Ravi algorithm | Python | PPI, seed genes and scores of all nodes |
Kwalk | Limited K-walks algorithm | Python | PPI, seed genes and scores of all nodes |