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Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network
Wen, YT (Wen, Yu-Ting); Lei, HJ (Lei, Hai-Jun); You, ZH (You, Zhu-Hong); Lei, BY (Lei, Bai-Ying); Chen, X (Chen, Xing); Li, LP (Li, Li-Ping)
2017
Source PublicationJOURNAL OF THEORETICAL BIOLOGY
ISSN0022-5193
Volume430Issue:10Pages:9-20
Abstract

Prediction of protein-protein interactions (PPIs) is of great significance. To achieve this, we propose a novel computational method for PPIs prediction based on a similarity network fusion (SNF) model for integrating the physical and chemical properties of proteins. Specifically, the physical and chemical properties of protein are the protein amino acid mutation rate and its hydrophobicity, respectively. The amino acid mutation rate is extracted using a BLOSUM62 matrix, which puts the protein sequence into block substitution matrix. The SNF model is exploited to fuse protein physical and chemical features of multiple data by iteratively updating each original network. Finally, the complementary features from the fused network are fed into a label propagation algorithm (LPA) for PPIs prediction. The experimental results show that the proposed method achieves promising performance and outperforms the traditional methods for the public dataset of H. pylori, Human, and Yeast. In addition, our proposed method achieves average accuracy of 76.65%, 81.98%, 84.56%, 84.01% and 84.38% on E. coli, C. elegans, H. sapien, H. pylori and M. musculus datasets, respectively. Comparison results demonstrate that the proposed method is very promising and provides a cost-effective alternative for predicting PPIs. The source code and all datasets are available at http://pan.baidu.comisil dF7rp7N.

KeywordProtein-protein Interactions Prediction Similarity Network Fusion Label Propagation Algorithm
DOI10.1016/j.jtbi.2017.06.003
Indexed BySCI
WOS IDWOS:000408401800002
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.xjipc.cas.cn/handle/365002/5032
Collection多语种信息技术研究室
Corresponding AuthorYou, ZH (You, Zhu-Hong)
Affiliation1.Shenzhen Univ, Coll Comp Sci & Software Engn, Shenzhen 518060, Guangdong, Peoples R China
2.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Peoples R China
3.Shenzhen Univ, Sch Biomed Engn, Shenzhen 518060, Guangdong, Peoples R China
4.Natl Reg Key Technol Engn Lab Med Ultrasound, Shenzhen 518060, Guangdong, Peoples R China
5.Guangdong Key Lab Biomed Measurements & Ultrasoun, Shenzhen 518060, Guangdong, Peoples R China
6.China Univ Min & Technol, Sch Informat & Control Engn, Xuzhou 21116, Jiangsu, Peoples R China
Recommended Citation
GB/T 7714
Wen, YT ,Lei, HJ ,You, ZH ,et al. Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network[J]. JOURNAL OF THEORETICAL BIOLOGY,2017,430(10):9-20.
APA Wen, YT ,Lei, HJ ,You, ZH ,Lei, BY ,Chen, X ,&Li, LP .(2017).Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network.JOURNAL OF THEORETICAL BIOLOGY,430(10),9-20.
MLA Wen, YT ,et al."Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network".JOURNAL OF THEORETICAL BIOLOGY 430.10(2017):9-20.
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