Table 2.
Main features of 20 typical clustering algorithms for extracting clusters from 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 | Functional module | Upon request | ||
| Van Dongen S 2000, Enright et al.2002 (MCL) | Flow simulation | √ | Protein family detection | http://micans.org/mcl/ | |
| Spirin and Mirny 2003 (SPC) | Hierarchical | √ | Protein complex | http://www.vcclab.org/lab/spc/ | |
| Bader and Hogue 2003 (MCODE) | Local neighbourhood density search | √ | Protein complex | http://baderlab.org/Software/MCODE | |
| King et al. 2004 (RNSC) | Local search cost based | Protein complex | upon request | ||
| Radicchi et al. 2004 (self contained G-N) | Hierarchical, module definition | 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 | http://www.cfinder.org/ | |
| 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 | http://kanaya.naist.jp/DPClus/ | |
| 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 | http://acgt.cs.tau.ac.il/matisse/ |
| Gregory 2007 (CONGA) | split betweenness | √ | Functional module | upon request | |
| Li et al.2008 (IPCA) | Local density and distance-based search | √ | Protein complex | http://netlab.csu.edu.cn/bioinformatics/limin/IPCA/ | |
| Mete et al. 2008 (SCAN) | structural clustering based on common neighbors | √ | Functional module | upon request | |
| Turanalp and Can 2008 (PPISpan) | gSpan | √ | √ | Frequent patterns | http://bioserver.ceng.metu.edu.tr/PPISpan/ |
| Li et al. 2009 (HC-Wpin) | Hierarchical clustering based on local metric | √ | Functional module | http://netlab.csu.edu.cn/bioinformatics/limin/HC-PIN/ | |