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SETS: A Seed-Dense-Expanding Model-Based Topological Structure for the Prediction of Overlapping Protein Complexes

Soheir Noori, Nabeel Al-A’araji and Eman Al-Shamery

Pertanika Journal of Science & Technology, Volume 29, Issue 2, April 2021

DOI: https://doi.org/10.47836/pjst.29.2.35

Keywords: Common neighbours; density; protein complex; protein–protein interaction network; topological structure

Published on: 30 April 2021

Defining protein complexes by analysing the protein–protein interaction (PPI) networks is a crucial task in understanding the principles of a biological cell. In the last few decades, researchers have proposed numerous methods to explore the topological structure of a PPI network to detect dense protein complexes. In this paper, the overlapping protein complexes with different densities are predicted within an acceptable execution time using seed expanding model and topological structure of the PPI network (SETS). SETS depend on the relation between the seed and its neighbours. The algorithm was compared with six algorithms on six datasets: five for yeast and one for human. The results showed that SETS outperformed other algorithms in terms of F-measure, coverage rate and the number of complexes that have high similarity with real complexes.

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ISSN 0128-7680

e-ISSN 2231-8526

Article ID

JST-2270-2020

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