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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
发表期刊JOURNAL OF THEORETICAL BIOLOGY
ISSN0022-5193
卷号430期号:10页码:9-20
摘要

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.

关键词Protein-protein Interactions Prediction Similarity Network Fusion Label Propagation Algorithm
DOI10.1016/j.jtbi.2017.06.003
收录类别SCI
WOS记录号WOS:000408401800002
引用统计
文献类型期刊论文
条目标识符http://ir.xjipc.cas.cn/handle/365002/5032
专题多语种信息技术研究室
通讯作者You, ZH (You, Zhu-Hong)
作者单位1.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
推荐引用方式
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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