Joining and decomposing reaction networks
Joining and decomposing reaction networks
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DOI：
10.1007/s00285-020-01477-y
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发表时间：
2020-03-02
影响因子：
1.9
通讯作者：
Shiu, Anne
中科院分区：
文献类型：
--
作者：
Gross, Elizabeth;Harrington, Heather;Shiu, Anne
在系统和合成生物学中，许多研究都集中在单一通路的行为和设计上，而最近，实验工作则集中在串扰（耦合两个或多个通路）或抑制分子功能（隔离通路的一部分）如何影响系统水平的行为。然而，处理这些大型系统的理论总体上已经落后。在这里，我们分析如何加入网络（例如，串扰）或分解网络（例如，抑制或敲除）影响反应网络可能具有的三种性质-可识别性（参数值从数据的可恢复性）、稳态不变量（稳态时物种浓度之间的关系，用于模型选择）和多稳态性（多稳态的能力，其对应于多个单元决策）。具体来说，我们证明的结果，澄清，通过加入两个较小的网络获得的网络，如何可以推断出或可以暗示原始网络的类似性质的较小的网络的属性。我们的证明使用计算代数几何的技术，包括消除理论和微分代数。
In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-level behavior. However, the theory for tackling these larger systems in general has lagged behind. Here, we analyze how joining networks (e.g., cross-talk) or decomposing networks (e.g., inhibition or knock-outs) affects three properties that reaction networks may possess-identifiability (recoverability of parameter values from data), steady-state invariants (relationships among species concentrations at steady state, used in model selection), and multistationarity (capacity for multiple steady states, which correspond to multiple cell decisions). Specifically, we prove results that clarify, for a network obtained by joining two smaller networks, how properties of the smaller networks can be inferred from or can imply similar properties of the original network. Our proofs use techniques from computational algebraic geometry, including elimination theory and differential algebra.