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Background  Protein complexes are the cornerstones of many biological processes and gather them to form various types of molecular machinery that perform a vast array of biological functions. In fact, a protein may belong to multiple protein complexes. Most existing protein complex detection algorithms cannot reflect overlapping protein complexes. To solve this problem, a novel overlapping protein complexes identification algorithm is proposed.    Results  In this paper, a new clustering algorithm based on overlay network chain in quotient space, marked as ONCQS, was proposed to detect overlapping protein complexes in weighted PPI networks. In the quotient space, a multilevel overlay network is constructed by using the maximal complete subgraph to mine overlapping protein complexes. The GO annotation data is used to weight the PPI network. According to the compatibility relation, the overlay network chain in quotient space was calculated. The protein complexes are contained in the last level of the overlay network. The experiments were carried out on four PPI databases, and compared ONCQS with five other state-of-the-art methods in the identification of protein complexes.    Conclusions  We have applied ONCQS to four PPI databases DIP, Gavin, Krogan and MIPS, the results show that it is superior to other five existing algorithms MCODE, MCL, CORE, ClusterONE and COACH in detecting overlapping protein complexes.

Detecting overlapping protein complexes in weighted PPI network based on overlay network chain in quotient space