Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster
Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster
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DOI：
10.1186/1752-0509-6-31
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发表时间：
2012-05-01
影响因子：
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通讯作者：
Cho, Kwang-Hyun
中科院分区：
文献类型：
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作者：
Kim, Man-Sun;Kim, Jeong-Rae;Cho, Kwang-Hyun
背景资料：网络模体为理解生物网络的功能原理提供了一种“概念工具”，但这种模体主要用于考虑静态网络结构。然而，静态网络不能用来揭示生物系统的时间和区域特异性特征。为了克服这一局限性，我们提出了“时空网络基序”的概念，时空序列的网络基序的子网络是活跃的，只有在特定的时间点和身体parts.Results：在这个概念的基础上，我们分析了果蝇胚胎的发育基因调控网络。我们确定了时空网络图案，并调查其在时间和空间上的分布模式。因此，我们发现了关键的发育过程是如何在时间和空间上受到基因网络的调控的。特别是，我们发现，嵌套的反馈回路经常出现在整个发展过程中。从数学模拟中，我们发现，相互抑制的嵌套反馈回路有助于形成的空间expression patterns.Conclusions：两者合计，所提出的概念和模拟可以用来解开发育基因调控网络的设计原则。
Background: Network motifs provided a "conceptual tool" for understanding the functional principles of biological networks, but such motifs have primarily been used to consider static network structures. Static networks, however, cannot be used to reveal time-and region-specific traits of biological systems. To overcome this limitation, we proposed the concept of a "spatiotemporal network motif," a spatiotemporal sequence of network motifs of sub-networks which are active only at specific time points and body parts.Results: On the basis of this concept, we analyzed the developmental gene regulatory network of the Drosophila melanogaster embryo. We identified spatiotemporal network motifs and investigated their distribution pattern in time and space. As a result, we found how key developmental processes are temporally and spatially regulated by the gene network. In particular, we found that nested feedback loops appeared frequently throughout the entire developmental process. From mathematical simulations, we found that mutual inhibition in the nested feedback loops contributes to the formation of spatial expression patterns.Conclusions: Taken together, the proposed concept and the simulations can be used to unravel the design principle of developmental gene regulatory networks.