Molecular interaction maps of bioregulatory networks: A general rubric for systems biology
Molecular interaction maps of bioregulatory networks: A general rubric for systems biology
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DOI：
10.1091/mbc.e05-09-0824
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发表时间：
2006-01-01
影响因子：
3.3
通讯作者：
Pommier, Y
中科院分区：
文献类型：
--
作者：
Kohn, KW;Aladjem, MI;Pommier, Y
生物调节网络图的标准是迫切需要的，就像电子学中需要电路图一样。已经提出了几种图形符号，但没有一种成为标准。我们已经使用分子相互作用图（MIM）符号准备了许多详细的生物调控网络图，我们现在相信它适合作为标准。在这里，我们正式描述MIM符号，并讨论其优点相对于替代方案。我们通过简单的例子展示了如何表示生物调控网络中常见的所有分子相互作用。MIM图有两种形式。“启发式”MIMs呈现了在时间和地点上共定位的分子可能的相互作用的库。“显式”MIM定义了用于计算机仿真的特定模型（从启发式MIM导出）。我们还展示了如何途径或过程可以突出一个典型的启发式MIM。绘制MIM图，坚持符号规则，强加了一个逻辑学科，加深了人们对网络结构和功能的理解。
A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the molecular interaction map (MIM) notation, and we now feel confident that it is suitable as a standard. Here, we describe the MIM notation formally and discuss its merits relative to alternative proposals. We show by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks. There are two forms of MIM diagrams. "Heuristic" MIMs present the repertoire of interactions possible for molecules that are colocalized in time and place. "Explicit" MIMs define particular models (derived from heuristic MIMs) for computer simulation. We show also how pathways or processes can be highlighted on a canonical heuristic MIM. Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network.