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Paper   IPM / Biological / 13210
School of Biological Sciences
  Title:   A Protein Complex Prediction Based On K-Connected Sub-Graphs In Protein Interaction Network
1.  M. Habibi.
2.  C. Eslahchi.
3.  L. Wong.
  Status:   Published
  Journal: BMC Systems Biology
  No.:  1
  Vol.:  4
  Year:  2010
  Pages:   129
  Supported by:  IPM
Background Protein complexes play an important role in cellular mechanisms. Recently, several methods have been presented to predict protein complexes in a protein interaction network. In these methods, a protein complex is predicted as a dense subgraph of protein interactions. However, interactions data are incomplete and a protein complex does not have to be a complete or dense subgraph.
Results We propose a more appropriate protein complex prediction method, CFA, that is based on connectivity number on subgraphs. We evaluate CFA using several protein interaction networks on reference protein complexes in two benchmark data sets (MIPS and Aloy), containing 1142 and 61 known complexes respectively. We compare CFA to some existing protein complex prediction methods (CMC, MCL, PCP and RNSC) in terms of recall and precision. We show that CFA predicts more complexes correctly at a competitive level of precision.
Conclusions Many real complexes with different connectivity level in protein interaction network can be predicted based on connectivity number. Our CFA program and results are freely available from http://www.bioinf.cs.ipm.ir/softwares/cfa/CFA.rar webcite.

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