CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning 
into Biclique Spanned Subgraphs

Omranian, N.; Nikoloski, Z.

doi:10.1007/978-3-030-93413-2_50

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CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning into Biclique Spanned Subgraphs

Omranian, N., & Nikoloski, Z. (2022). CUBCO: Prediction of Protein Complexes Based on Min-cut Network Partitioning into Biclique Spanned Subgraphs. Cham: Springer International Publishing.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0009-BFF2-F Version Permalink: https://hdl.handle.net/21.11116/0000-000C-2813-2

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Creators:
Omranian, N.¹, Author
Nikoloski, Z.¹, Author

Affiliations:
1Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753310

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Abstract: High-throughput approaches have generated large-scale protein-protein interaction (PPI) networks that are used in prediction of protein complexes. Here, we introduce CUBCO—a minimum cut-based algorithm that predicts protein complexes as biclique spanned subgraphs while relying on link prediction approaches to score and incorporate missing interactions. Our comprehensive analyses with PPIs from different organisms show that CUBCO performs on par with the best-performing approaches, that model protein complexes as biclique spanned subgraphs, and outperforms the remaining contenders. We also show that the usage of link prediction approaches in CUBCO improves the prediction of protein complexes on average 34.22% in all comparisons. Finally, CUBCO recovers ~40% and ~11% of known protein complexes from the Pan-Plant and Metazoan PPI networks. Therefore, CUBCO represents an efficient, parameter-free approach for accurate prediction of protein complexes from PPI networks.

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Language(s): eng - English

Dates: Date issued: 2022-01-01

Publication Status: Issued

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Publishing info: Cham : Springer International Publishing

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Identifiers: DOI: 10.1007/978-3-030-93413-2_50

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Title: Studies in Computational Intelligence

Source Genre: Proceedings

Creator(s):
Benito, Rosa Maria, Editor
Cherifi, Chantal, Editor
Cherifi, Hocine, Editor
Moro, Esteban, Editor
Rocha, Luis M., Editor
Sales-Pardo, Marta, Editor

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Title: Complex Networks & Their Applications X

Source Genre: Proceedings

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Pages: - Volume / Issue: 1016 Sequence Number: - Start / End Page: 605 - 615 Identifier: -