Identification of protein complexes and functional modules in E. coli PPI networks

BMC Microbiology

article

Kong, Ping¹  Huang, Gang¹  Liu, Wei² 

[1] Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences;Research Center for Intelligence Information Technology, Nantong University;School of Mathematics and Statistics Science, Lu Dong University

关键词: Protein complexes;    Functional modules;    Link clustering algorithm;    E;    coli PPI networks;   

DOI  :  10.1186/s12866-020-01904-6

学科分类：放射科、核医学、医学影像

来源: BioMed Central

【 摘 要 】

Escherichia coli always plays an important role in microbial research, and it has been a benchmark model for the study of molecular mechanisms of microorganisms. Molecular complexes, operons, and functional modules are valuable molecular functional domains of E. coli. The identification of protein complexes and functional modules of E. coli is essential to reveal the principles of cell organization, process, and function. At present, many studies focus on the detection of E. coli protein complexes based on experimental methods. However, based on the large-scale proteomics data set of E. coli, the simultaneous prediction of protein complexes and functional modules, especially the comparative analysis of them is relatively less. In this study, the Edge Label Propagate Algorithm (ELPA) of the complex biological network was used to predict the protein complexes and functional modules of two high-quality PPI networks of E. coli, respectively. According to the gold standard protein complexes and function annotations provided by EcoCyc dataset, most protein modules predicted in the two datasets matched highly with real protein complexes, cellular processes, and biological functions. Some novel and significant protein complexes and functional modules were revealed based on ELPA. Moreover, through a comparative analysis of predicted complexes with corresponding functional modules, we found the protein complexes were significantly overlapped with corresponding functional modules, and almost all predicted protein complexes were completely covered by one or more functional modules. Finally, on the same PPI network of E. coli, ELPA was compared with a well-known protein module detection method (MCL) and we found that the performance of ELPA and MCL is comparable in predicting protein complexes. In this paper, a link clustering method was used to predict protein complexes and functional modules in PPI networks of E. coli, and the correlation between them was compared, which could help us to understand the molecular functional units of E. coli better.

【 授权许可】

CC BY|CC0