From: Recent advances in clustering methods for protein interaction networks
Authors | Methods | Weighted graphs supported | Overlapping clusters supported | Objective | Web-Tool Available |
---|---|---|---|---|---|
Girvan and Newman 2002 (G-N) | Hierarchical clustering based on betweenness | Â | Â | Functional module | Upon request |
Van Dongen S 2000, Enright et al.2002 (MCL) | Flow simulation | √ |  | Protein family detection | |
Spirin and Mirny 2003 (SPC) | Hierarchical | √ |  | Protein complex | |
Bader and Hogue 2003 (MCODE) | Local neighbourhood density search |  | √ | Protein complex | |
King et al. 2004 (RNSC) | Local search cost based | Â | Â | Protein complex | upon request |
Radicchi et al. 2004 (self contained G-N) | Hierarchical, module definition | Â | Â | Strong module or weak module | upon request |
Pržulj et al. 2004 | Minimum cut (HCS) |  |  | Protein complex | upon request |
Palla et al. 2005 (CPM) | Clique Percolation |  | √ | Protein complex; functional module | |
Li et al. 2005 (LCMA) | Local clique merging |  | √ | Protein complex | upon request |
Altaf-UI-Amin et al. 2006 (DPClus) | Local density and periphery search |  | √ | Protein complex | |
Hwang et al. 2006 (STM) | signal transduction |  | √ | Functional module | upon request |
Zotenko et al. 2006 (COD) | Complex Overlap Decomposition |  | √ | Protein complex | upon request |
Luo et al. 2007 (MoNet) | Hierarchical, module definition |  | √ | Functional module | upon request |
Cho et al. 2007 (Semantic integration) | flow-based clustering and Semantic integration | √ | √ | Functional module | upon request |
Ulitsky and Shamir 2007 (MATISSE) | Module Analysis via Topology of Interactions and Similarity | √ | √ | Functional module | |
Gregory 2007 (CONGA) | split betweenness |  | √ | Functional module | upon request |
Li et al.2008 (IPCA) | Local density and distance-based search |  | √ | Protein complex | |
Mete et al. 2008 (SCAN) | structural clustering based on common neighbors |  | √ | Functional module | upon request |
Turanalp and Can 2008 (PPISpan) | gSpan | √ | √ | Frequent patterns | |
Li et al. 2009 (HC-Wpin) | Hierarchical clustering based on local metric | √ |  | Functional module |