A method for identifying protein complexes with the features of joint co-localization and joint co-expression in static PPI networks

A method for identifying protein complexes with the features of joint co-localization and joint co-expression in static PPI networks

Zhang, Jinxiong (South China University of Technology; Guangxi University)
Zhong, Cheng (Guangxi University)
Huang, Yiran (Guangxi University)
Lin, H.X. (TU Delft Mathematical Physics)
Wang, Mian (Guangxi University)

2019

Identifying protein complexes in static protein-protein interaction (PPI) networks is essential for understanding the underlying mechanism of biological processes. Proteins in a complex are co-localized at the same place and co-expressed at the same time. We propose a novel method to identify protein complexes with the features of joint co-localization and joint co-expression in static PPI networks. To achieve this goal, we define a joint localization vector to construct a joint co-localization criterion of a protein group, and define a joint gene expression to construct a joint co-expression criterion of a gene group. Moreover, the functional similarity of proteins in a complex is an important characteristic. Thus, we use the CC-based, MF-based, and BP-based protein similarities to devise functional similarity criterion to determine whether a protein is functionally similar to a protein cluster. Based on the core-attachment structure and following to seed expanding strategy, we use four types of biological data including PPI data with reliability score, protein localization data, gene expression data, and gene ontology annotations, to identify protein complexes. The experimental results on yeast data show that comparing with existing methods our proposed method can efficiently and exactly identify more protein complexes, especially more protein complexes of sizes from 2 to 6. Furthermore, the enrichment analysis demonstrates that the protein complexes identified by our method have significant biological meaning.

Core-attachment structure
Joint co-expression
Joint co-localization
Protein complexes
Seed expanding strategy
Static PPI networks

http://resolver.tudelft.nl/uuid:0e031e5c-01b3-4f05-b99d-022ae45b05b5

https://doi.org/10.1016/j.compbiomed.2019.103333

2020-07-31

0010-4825

Computers in Biology and Medicine, 111, 1-19

Accepted author manuscript

Institutional Repository

journal article

© 2019 Jinxiong Zhang, Cheng Zhong, Yiran Huang, H.X. Lin, Mian Wang