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翁宇豪, 陈铭
Application of multilayer network in protein-protein interaction networks (PPI) of rice and cancer
WENG Yuhao, CHEN Ming
(Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China)
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摘要: 网络是研究系统间连接结构的学科方法与研究技术。本文介绍单层网络和多层网络模型的数学理论,以及多层网络中多重度、重叠度与激活度、重叠性、度关联函数、参与系数以及度相关系数的概念,并将这些分析方法运用到了水稻细胞、癌症细胞和正常组织的蛋白质互作网络(protein-protein interaction networks,PPI)中,研究它们的特殊结构与性质。在水稻的蛋白质互作网络中,发现它的重叠度与激活度呈幂律分布;通过参与系数的分析发现了与细胞整体功能相关的重要蛋白质;通过相关系数热图分析发现了关联性较强的细胞器以及关联性较弱的细胞器。在癌症组织PPI以及正常组织中,通过重叠性图谱分析和核心网络比对的方法,发现了癌症网络的核心网络的规模比正常组织大,且具有强核心结构、高度均质性以及不易受到攻击而崩溃的特点;发现了非平凡的重叠度和激活度分布,并分析了癌症与正常组织在结构和功能上的差异。
Abstract: Network is a disciplinary methodology to study the connecting patterns of complex systems. Network science has developed fast and obtained surprising results in lots of areas. However, single-layer network is powerless facing various relationships in real systems. Therefore, it is necessary to create a new model to break the bottleneck. This paper describes the multilayer network which is powerful in dealing with these problems.
  Most protein interactions in organisms can be simplified as networks (PPI), but we can not locate each protein specifically in a single-layer PPI network model which makes it difficult to study the difference between PPI in special regions in an organism and the whole PPI in an organism. We divided the rice cell into several organelles to study the relationship between organelles and cell functions. Moreover, we used different cancer tissues and normal tissues in human body to construct two multilayer PPI and study the underlying mechanics of cancer comparing with the normal tissues.
  We introduced the mathematical theories of multilayer networks along with the concept of multi-degree, overlap of edge, activity of node, multiplexity, degree correlation, participation coefficient and degree correlation coefficient, which are used to analyze the nontrivial structure and properties in PPIs of rice, cancer and normal tissue.
  In rice PPIs, we investigated the power-law distribution of edge overlap and node activity, and found important proteins related to functional organelles in cell by analyzing participation coefficient, and organelles of strong correlations or weak correlations by analyzing heat map of layer's degree. In PPIs of cancer and normal tissue, we discovered that there are strong core structure, high homogeneousness and robustness in cancer by multiplexity diagram analysis and alignment of core networks, and the nontrivial distribution of overlap and activity. There are more core proteins in cancer than in normal tissues and various types of cancers have mostly the same core structure along with the degeneration of tissue-specified proteins. It is indicated that the core structure of cancer PPIs is related to cell proliferation, growth and transfer. Moreover, different cancers have their own specified proteins that are probably encoded by different oncogenes which lead to series of gene expressions and biochemical reactions during the formation of the same core network.
  The former results showed that multilayer networks is a creative and powerful tool in studying complex systems and can be used in biology widely to find nontrivial properties and mechanism of biology phenomenon.
出版日期: 2017-01-25
CLC:  Q 2  
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翁宇豪, 陈铭. 多层网络模型在水稻与癌症蛋白质互作网络中的应用[J]. 浙江大学学报(农业与生命科学版), 10.3785/j.issn.1008-9209.2016.06.071.

WENG Yuhao, CHEN Ming. Application of multilayer network in protein-protein interaction networks (PPI) of rice and cancer. Journal of Zhejiang University (Agriculture and Life Sciences), 10.3785/j.issn.1008-9209.2016.06.071.


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