发表机构
Universal Biology Institute, The University of Tokyo; Indian Institute of Engineering Science and Technology, Shibpur; Bose Institute（东京大学通用生物学研究所; 印度工程科学和技术学院，希布普尔分校; 玻色研究所）
机构由 AI 辅助整理，请以论文原文为准。AI 中文总结
本研究提出信息论框架，通过干扰互信息（IMI）解释大肠杆菌和酿酒酵母转录网络中前馈环的丰度模式，发现IMI与丰度高度吻合，揭示了信息处理与鲁棒性的权衡关系。
AI 中文摘要
生物网络存在反复出现的基序，但其丰度不均的现象仍未被充分理解。前馈环（FFL）是大肠杆菌（Escherichia coli）和酿酒酵母（Saccharomyces cerevisiae）转录网络中的重要基序，然而其八种类型的出现频率极不均衡。本研究提出一种信息论框架，将输入-输出互信息分解为通路分量和干扰分量。干扰互信息（IMI）量化直接与间接调控通路对信息传递的联合影响。结果显示，在两种生物中，IMI与观测到的丰度模式高度吻合，而输入-输出互信息及通路分量则不具备此特性。我们还将IMI的层级追溯至通路-干扰相互作用的强度及局部通路敏感性。值得注意的是，更强的IMI还与参数变化下鲁棒性降低相关，表明基因调控回路中存在信息处理与恢复力之间的权衡。因此，我们的结果确定了一种与丰度模式相关的、依赖拓扑结构的信息论特征。
英文摘要
In the transcriptional networks of \textit{Escherichia coli} and \textit{Saccharomyces cerevisiae}, the eight feed-forward loop (FFL) motifs occur at markedly different frequencies. Although previous studies have linked the abundant C1- and I1-FFLs to specific dynamical functions, a common account of the broader pattern is lacking. To address this gap, we adopt an information-theoretic approach. An FFL transmits information through two paths that share an input and converge on an output, suggesting that their interaction may contribute to differences among motifs. To investigate this, we decompose input-output mutual information (MI) into pathway MI and interference MI (IMI). Here, the pathway MI collects the contributions of individual pathways, whereas IMI identifies the contribution that arises from their interference. We find that within a representative parameter regime, IMI values of FFLs produce a hierarchy that closely resembles the abundance ordering in \textit{E. coli}, whereas total and pathway MIs do not. Motivated by this observation, we perform constrained optimization that identifies parameter regimes compatible with abundance-like targets for both \textit{S. cerevisiae} and \textit{E. coli}. We relate the optimized IMI hierarchy to pathway interference strength and local pathway sensitivities to understand the underlying biophysical origin. Our framework thus probes the correspondence between pathway interference, information transmission, and motif-abundance hierarchies.
Comments39 pages, 14 figures
