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Complex Prediction in Large PPI Networks Using Expansion and Stripe of Core Cliques

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Abstract

The widespread availability and importance of large-scale protein-protein interaction (PPI) data demand a flurry of research efforts to understand the organisation of a cell and its functionality by analysing these data at the network level. In the bioinformatics and data mining fields, network clustering acquired a lot of attraction to examine a PPI network’s topological and functional aspects. The clustering of PPI networks has been proven to be an excellent method for discovering functional modules, disclosing functions of unknown proteins, and other tasks in numerous research over the last decade. This research proposes a unique graph mining approach to detect protein complexes using dense neighbourhoods (highly connected regions) in an interaction graph. Our technique first finds size-3 cliques associated with each edge (protein interaction), and then these core cliques are expanded to form high-density subgraphs. Loosely connected proteins are stripped out from these subgraphs to produce a potential protein complex. Finally, the redundancy is removed based on the Jaccard coefficient. Computational results are presented on the yeast and human protein interaction dataset to highlight our proposed technique’s efficiency. Predicted protein complexes of the proposed approach have a significantly higher score of similarity to those used as gold standards in the CYC-2008 and CORUM benchmark databases than other existing approaches.

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Acknowledgements

We acknowledge the infrastructure and computational facilities received from DST-FIST Bioinformatics Lab of IIIT Bhubaneswar.

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  1. Swati Vipsita, Sabyasachi Patra have contributed equally to this work.

Authors and Affiliations

  1. CSE, IIIT Bhubaneswar, Gothapatna, Bhubaneswar, Odisha, 751003, India

    Tushar Ranjan Sahoo, Swati Vipsita & Sabyasachi Patra

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  1. Tushar Ranjan Sahoo
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Sahoo, T.R., Vipsita, S. & Patra, S. Complex Prediction in Large PPI Networks Using Expansion and Stripe of Core Cliques. Interdiscip Sci Comput Life Sci 15, 331–348 (2023). https://doi.org/10.1007/s12539-022-00541-z

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