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DPCMNE: detecting protein complexes from protein-protein interaction networks via multi-level network embedding

DPCMNE: detecting protein complexes from protein-protein interaction networks via multi-level network embedding

Authors :
Ju Xiang
Fang-Xiang Wu
Xiangmao Meng
Min Li
Ruiqing Zheng
Source :
IEEE/ACM Transactions on Computational Biology and Bioinformatics. :1-1
Publication Year :
2021
Publisher :
Institute of Electrical and Electronics Engineers (IEEE), 2021.

Abstract

Biological functions of a cell are typically carried out through protein complexes. The detection of protein complexes is therefore of great significance for understanding the cellular organizations and protein functions. In the past decades, many computational methods have been proposed to detect protein complexes. However, most of the existing methods just search the local topological information to mine dense subgraphs as protein complexes, ignoring the global topological information. To tackle this issue, we propose the DPCMNE method to detect protein complexes via multi-level network embedding. It can preserve both the local and global topological information of biological networks. First, DPCMNE employs a hierarchical compressing strategy to recursively compress the input protein-protein interaction (PPI) network into multi-level smaller PPI networks. Then, a network embedding method is applied on these smaller PPI networks to learn protein embeddings of different levels of granularity. The embeddings learned from all the compressed PPI networks are concatenated to represent the final protein embeddings of the original input PPI network. Finally, a core-attachment based strategy is adopted to detect protein complexes in the weighted PPI network constructed by the pairwise similarity of protein embeddings. To assess the efficiency of our proposed method, DPCMNE is compared with other eight clustering algorithms on two yeast datasets. The experimental results show that the performance of DPCMNE outperforms those state-of-the-art complex detection methods in terms of F1 and F1+Acc. Furthermore, the results of functional enrichment analysis indicate that protein complexes detected by DPCMNE are more biologically significant in terms of P-score.

Details

ISSN :
23740043 and 15455963
Database :
OpenAIRE
Journal :
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Accession number :
edsair.doi.dedup.....d187cff9434449a1cb94217f97878ac5
Full Text :
https://doi.org/10.1109/tcbb.2021.3050102