Table 2 Main features of 20 typical clustering algorithms for extracting clusters from protein interaction networks.

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/