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  • Title: Protein complexes detection based on node local properties and gene expression in PPI weighted networks.
    Author: Yu Y, Kong D.
    Journal: BMC Bioinformatics; 2022 Jan 06; 23(1):24. PubMed ID: 34991441.
    Abstract:
    BACKGROUND: Identifying protein complexes from protein-protein interaction (PPI) networks is a crucial task, and many related algorithms have been developed. Most algorithms usually employ direct neighbors of nodes and ignore resource allocation and second-order neighbors. The effective use of such information is crucial to protein complex detection. RESULT: Based on this observation, we propose a new way by combining node resource allocation and gene expression information to weight protein network (NRAGE-WPN), in which protein complexes are detected based on core-attachment and second-order neighbors. CONCLUSIONS: Through comparison with eleven methods in Yeast and Human PPI network, the experimental results demonstrate that this algorithm not only performs better than other methods on 75% in terms of f-measure+, but also can achieve an ideal overall performance in terms of a composite score consisting of five performance measures. This identification method is simple and can accurately identify more complexes.
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