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主管单位 工业和信息化部 主办单位 哈尔滨工业大学 主编 任南琪 国际刊号ISSN 1672-5565 国内刊号CN 23-1513/Q

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引用本文:李雷,蒋林华.基于Cytoscape下斑马鱼衰老基因-蛋白质的模块化分析[J].生物信息学,2019,17(3):175-181.
LI lei,JIANG Linhua.Modular analysis of zebrafish senescence gene-protein based on Cytoscape[J].Chinese Journal of Bioinformatics,2019,17(3):175-181.
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基于Cytoscape下斑马鱼衰老基因-蛋白质的模块化分析
李雷, 蒋林华
(上海理工大学 现代光学系统重点实验室,上海 200093)
摘要:
近20年来,斑马鱼逐渐成为研究人类基因功能的重要模型动物。同时,通过对斑马鱼参考基因组序列和10 000多个蛋白编码基因的鉴定,表明斑马鱼至少与人类基因有75%的同源性,进一步验证了斑马鱼基因组序列可以作为衰老的研究模型。此外,其良好保守的分子和细胞生理学的广泛特征使斑马鱼成为揭示衰老、疾病和修复的潜在机制的极好模型。但是斑马鱼衰老的分子机制很少发生分子间的相互作用,因此蛋白质-蛋白相互作用(PPI)网络是非常可取的。本实验描述了斑马鱼这种生物衰老机制的模型,其涵盖了与衰老相关的87种蛋白质之间的767种相互作用。这不仅包含准确预测的PPI,还包含从文献收集以及实验所得的那些分子相互作用。同时,将这些分子相互作用模块化,形成模块化,找到11个中心基因,分析预测其衰老过程。希望能帮助研究斑马鱼的学者研究其衰老过程,提供一些假说和帮助。
关键词:  斑马鱼  衰老分子机制  PPI  模块化  中枢基因
DOI:10.12113/j.issn.1672-5565.201901001
分类号:Q344+.13
文献标识码:A
基金项目:国家自然科学基金上海市高等学校特聘教授项目(东方学者,15HJPY-MS02, No.61775139).
Modular analysis of zebrafish senescence gene-protein based on Cytoscape
LI lei , JIANG Linhua
(Shanghai Key Lab of Modern Optical Systems, University of Shanghai for Science and Technology, Shanghai 200093,China)
Abstract:
In the past 20 years, zebrafish has gradually become an important model animal to study the function of human genes. Meanwhile, through the identification of zebrafish reference genome sequence and more than 0,0 protein-coding genes, it shows that zebrafish has at least 75% homology with human genes, which further proves that zebrafish genome sequence can be used as a research model of aging. In addition, its well-conserved molecular and cellular physiology of a wide range of characteristics make zebrafish an excellent model for revealing the underlying mechanisms of aging, disease, and repair. However, molecular mechanisms of zebrafish senescence rarely involve intermolecular interactions, so the protein-protein interaction (PPI) network is a highly desirable option. This paper describes a model of the biological aging mechanism of zebrafish, which covers 767 interactions between 87 proteins related to aging. This not only includes accurately predicted PPI, but also those molecular interactions from literature collection and experiments. At the same time, these molecular interactions were modularized to form modularity, and 11 central genes were found to analyze and predict the aging process. The paper aims to help researchers of zebrafish study the aging process and provide some hypotheses and help.
Key words:  Zebrafish  Senescence molecular mechanism  PPI  Modular  Central genes

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