Detecting overlapping protein complexes in protein-protein interaction networks
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Updated: May 24, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
Published on: March 3, 2015
Tamás Nepusz1, Haiyuan Yu, Alberto Paccanaro
1Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK.
Abstract:
We introduce clustering with overlapping neighborhood expansion (ClusterONE), a method for detecting potentially overlapping protein complexes from protein-protein interaction data. ClusterONE-derived complexes for several yeast data sets showed better correspondence with reference complexes in the Munich Information Center for Protein Sequence (MIPS) catalog and complexes derived from the Saccharomyces Genome Database (SGD) than the results of seven popular methods. The results also showed a high extent of functional homogeneity.
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