TY - JOUR
T1 - Characterization of protein complexes and subcomplexes in protein-protein interaction databases
AU - Zaki, Nazar
AU - Mohamed, Elfadil A.
AU - Mora, Antonio
N1 - Publisher Copyright:
© 2015 Nazar Zaki et al.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
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U2 - 10.1155/2015/245075
DO - 10.1155/2015/245075
M3 - Article
AN - SCOPUS:84924311449
SN - 2090-2247
VL - 2015
JO - Biochemistry Research International
JF - Biochemistry Research International
M1 - 245075
ER -