[1]LIU Guangming,YANG Liu,GAO Panpan,et al.The functional module detection of PPI network by incorporating protein complex data[J].CAAI Transactions on Intelligent Systems,2016,11(5):703-710.[doi:10.11992/tis.201603034]
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The functional module detection of PPI network by incorporating protein complex data
CAAI Transactions on Intelligent Systems[ISSN 1673-4785/CN 23-1538/TP] Volume:
11
Number of periods:
2016 5
Page number:
703-710
Column:
学术论文—脑认知基础
Public date:
2016-11-01
- Title:
- The functional module detection of PPI network by incorporating protein complex data
- Keywords:
- PPI; protein complex; functional module; module detection; gene ontology; pathway
- CLC:
- TP391
- DOI:
- 10.11992/tis.201603034
- Abstract:
- Functional module detection of protein-protein interaction (PPI) network has been a major challenge identified recently by medical researchers. It allows understanding and recognizing the interaction between proteins in an efficient manner. In this study, topological module detection methods, popular in the field of complex protein networks, were applied to the PPI network to obtain these modules, followed by a biological analysis of the topological modules. The interaction mechanism was observed for only 10%~20% of the protein pairs because of incomplete PPI data. Furthermore, the data for noise interaction always existed in PPI; therefore, the number of biologically precise modules decreased according to topological community-detection methods. In this study, the protein complex data was incorporated into the PPI network to identify more biologically precise protein modules. K-Means clustering and non-negative matrix factorization algorithms were used to segregate the PPI network into different modules. Gene ontology (GO) and pathway analysis were conducted for each of these modules to quantify their biological significance. The results of the experiments showed that the modules detected by combining the protein complex and PPI network demonstrate a higher tendency to achieve larger homogeneity values compared with those detected using GO and pathway analysis.
- References:
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1900-01-01