Network motifs: structure does not determine function.
Network motifs: structure does not determine function.
复制标题
网络图案：结构无法确定功能。
DOI：
10.1186/1471-2164-7-108
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发表时间：
2006-05-05
期刊：
影响因子：
4.4
通讯作者：
Stark, Jaroslav
中科院分区：
文献类型：
--
作者：
Ingram, Piers J;Stumpf, Michael P H;Stark, Jaroslav
一些出版物最近研究了前馈基序在各种网络中的发生和性质，包括那些在基因组生物学中感兴趣的网络，如基因网络。目前的工作期待在一些细节的bi-fan基序的动力学，使用系统的常微分方程模型的转录因子，mRNA和蛋白质的群体，目的是扩展我们的理解似乎是重要的基因网络结构的基石。我们开发了一个常微分方程模型的bi-fan主题和分析变体的主题对应于其在各种条件下的行为。特别是，我们研究了不同的稳定和脉冲输入的影响，五个变种的bifan图案，在文献中发现的酿酒酵母（俗称面包酵母）的bifan图案的证据的基础上。使用这个模型，我们的特点的bi-fan图案的动力学行为的生物合理的参数和配置范围广泛。我们发现，没有特征行为的主题，并与正确选择的参数和内部结构，非常不同的，甚至相反的行为可能会得到。即使在这个相对简单的模型中，双扇图案也可以表现出广泛的动态响应。这表明，仅仅通过考虑基因网络的连接结构或将其分解为简单的结构基序，很难获得对生物功能的重要见解。有必要通过动力学参数或动态时间序列实验数据来补充这种结构信息，这两者目前都很难获得。
A number of publications have recently examined the occurrence and properties of the feed-forward motif in a variety of networks, including those that are of interest in genome biology, such as gene networks. The present work looks in some detail at the dynamics of the bi-fan motif, using systems of ordinary differential equations to model the populations of transcription factors, mRNA and protein, with the aim of extending our understanding of what appear to be important building blocks of gene network structure. We develop an ordinary differential equation model of the bi-fan motif and analyse variants of the motif corresponding to its behaviour under various conditions. In particular, we examine the effects of different steady and pulsed inputs to five variants of the bifan motif, based on evidence in the literature of bifan motifs found in Saccharomyces cerevisiae (commonly known as baker's yeast). Using this model, we characterize the dynamical behaviour of the bi-fan motif for a wide range of biologically plausible parameters and configurations. We find that there is no characteristic behaviour for the motif, and with the correct choice of parameters and of internal structure, very different, indeed even opposite behaviours may be obtained. Even with this relatively simple model, the bi-fan motif can exhibit a wide range of dynamical responses. This suggests that it is difficult to gain significant insights into biological function simply by considering the connection architecture of a gene network, or its decomposition into simple structural motifs. It is necessary to supplement such structural information by kinetic parameters, or dynamic time series experimental data, both of which are currently difficult to obtain.