Characterization of protein complexes and subcomplexes in protein-protein interaction databases

Nazar Zaki, Elfadil A. Mohamed, Antonio Mora

    Research output: Contribution to journalArticlepeer-review

    1 Citation (Scopus)

    Abstract

    The identification and characterization of protein complexes implicated in protein-protein interaction data are crucial to the understanding of the molecular events under normal and abnormal physiological conditions. This paper provides a novel characterization of subcomplexes in protein interaction databases, stressing definition and representation issues, quantification, biological validation, network metrics, motifs, modularity, and gene ontology (GO) terms. The paper introduces the concept of "nested group" as a way to represent subcomplexes and estimates that around 15% of those nested group with the higher Jaccard index may be a result of data artifacts in protein interaction databases, while a number of them can be found in biologically important modular structures or dynamic structures. We also found that network centralities, enrichment in essential proteins, GO terms related to regulation, imperfect 5-clique motifs, and higher GO homogeneity can be used to identify proteins in nested complexes.

    Original languageEnglish
    Article number245075
    JournalBiochemistry Research International
    Volume2015
    DOIs
    Publication statusPublished - 2015

    ASJC Scopus subject areas

    • Biochemistry

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