Table 2.
Main features of the graph clustering methods presented in this study
| Markov clustering (MCL) | Restricted Neighborhood Search Clustering (RNSC) | Laplacian dynamics (LD) | Cartographic Representation (CR) | Genetic Algorithm to find communities in Protein-Protein Interaction networks (GAPPI) | |
|---|---|---|---|---|---|
| Type | Flow simulation & Pagerank centrality | Cost-based local search | Multiscale modular structure | Inter- and intramodule connection | Search inspired by natural evolution |
| Allow multiple assignations | No | No | No | No | No |
| Allow unassigned nodes | No | No | No | No | No |
| Edge-weighted graphs supported | Yes | No | Yes | No | No |
| First application | Protein family detection | Protein complex prediction | High modularity partitions of large (more than million) networks finding | Metabolic network | Protein-protein interaction networks |
| Availability | http://rsat.scmbb.ulb.ac.be/rsat/index_neat.html | http://rsat.scmbb.ulb.ac.be/rsat/index_neat.html | Upon Gephi program | Upon request | http://staff.icar.cnr.it/pizzuti/codes.html |
| Developer (Year) | Enright A.J. et al. (2002) [19] | King A.D. et al. (2004) [20] | (1) Lambiotte R. et al. (2007) [49]; | Guimera R. & Amaral LAN (2005) [47] | Pizzuti C. & Rombo S. E. (2014) [16] |
| (2) Blondel V.D. et al. (2008) [48] |