access icon openaccess Identification of essential proteins based on a new combination of topological and biological features in weighted protein–protein interaction networks

This is an open access article published by the IET under the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/)
Received 29/01/2018, Accepted 30/04/2018, Revised 23/04/2018, Published 15/06/2018

The identification of essential proteins in protein–protein interaction (PPI) networks is not only important in understanding the process of cellular life but also useful in diagnosis and drug design. The network topology-based centrality measures are sensitive to noise of network. Moreover, these measures cannot detect low-connectivity essential proteins. The authors have proposed a new method using a combination of topological centrality measures and biological features based on statistical analyses of essential proteins and protein complexes. With incomplete PPI networks, they face the challenge of false-positive interactions. To remove these interactions, the PPI networks are weighted by gene ontology. Furthermore, they use a combination of classifiers, including the newly proposed measures and traditional weighted centrality measures, to improve the precision of identification. This combination is evaluated using the logistic regression model in terms of significance levels. The proposed method has been implemented and compared to both previous and more recent efficient computational methods using six statistical standards. The results show that the proposed method is more precise in identifying essential proteins than the previous methods. This level of precision was obtained through the use of four different data sets: YHQ-W, YMBD-W, YDIP-W and YMIPS-W.

Inspec keywords: drugs; topology; biology computing; proteins; ontologies (artificial intelligence)

Other keywords: weighted centrality measures; YMBD-W dataset; protein complexes; biological features; low-connectivity essential proteins; incomplete PPI networks; YMIPS-W dataset; YHQ-W dataset; network topology-based centrality measures; YDIP-W dataset; weighted protein–protein interaction networks; topological centrality measures

Subjects: Knowledge engineering techniques; Combinatorial mathematics; Biology and medical computing

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