一种新的无标度网络构建方法及其在基因表达谱模拟上的应用(英文)  

A Novel Scale-free Network Construction Method and Its Application in Gene Expression Profiles Simulation

作　　者：郑明[1] 黄艳新[2] 沈威[1,3] 钟毅[1] 吴佳楠[1,4] 刘桂霞[1] 周柚[1] 

机构地区：[1]吉林大学计算机科学与技术学院,符号计算与知识工程教育部重点实验室,长春130012 [2]东北师范大学药物基因和蛋白质筛选国家工程实验室,长春130024 [3]北华大学计算机科学与技术学院,吉林132021 [4]长春大学计算机科学与技术学院,长春130012

出　　处：《生物化学与生物物理进展》2012年第6期581-590,共10页Progress In Biochemistry and Biophysics

基　　金：supported by grants from The National Natural Science Foundation of China(60873146,60973092,60903097,61172183);Hi-Tech Research and Development Program of China(2009AA02Z307);Project of Science and Technology Innovation Platform of Computing and Software Science(985 Engineering);The Key Laboratory for Symbol Computation and Knowledge Engineering of the National Education Ministry of China;Graduate Innovation Fund of Jilin University(20111062);Natural Science Foundation of Jilin Province(20101503)~~

摘　　要：本文提出一种新的基于重连接方法的无标度网络构建算法.根据重连接方法新节点的调控节点会被重选,重连接概率取决于幂率分布模型参数gamma.用本文算法构建的网络通过微分方程模型来模拟基因表达谱数据,所用的优化算法为GA与PSO.候选节点的选择可以根据已有节点的连接数决定.实验的网络可以用log-log图,模拟的基因表达谱也用微分方程模型来验证效果.每个连接的正确性将会通过实验验证,完整的程序可以通过我们的官方网站获得:http://ccst.jlu.edu.cn/CSBG/ourown/.In this paper, a novel scale-free network construction algorithm based on reconnection method was proposed. The regulatory node of the new node will be reselected according to the reconnection method. The probability of reconnection depends on the gamma in the power-law distribution model parameters. The constructed network with our algorithm was used for simulating gene expression profiles using differential equation model with two heuristic search algorithms, GA and PSO, and new algorithm GFA to optimize the criterion. The candidate old node can be selected as regulatory node based on the number of links the old node already has. The network in the experiment was testified using log-log graph. And the simulated gene expression pi＇ofiles were also tested with three different well developed algorithms＇ software available free from intemet by reconstructing the network. PPV and Se of the links were calculated and visualized. A part of the results and the full version program written by java could be downloaded from our website： http：//cest.jlu.edu.cn/CSBG/ourown/.

关 键 词：基因表达谱 无标度网络 重连接 微分方程模型 启发式搜索 

分 类 号：Q67[生物学—生物物理学] TP18[自动化与计算机技术—控制理论与控制工程]