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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation
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A Modeling Framework for Generation of Positional and Temporal Simulations of Transcriptional Regulation

机译：转录调控的位置和时间模拟生成的建模框架

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摘要

We present a modeling framework aimed at capturing both the positional and temporal behavior of transcriptional regulatory proteins in eukaryotic cells. There is growing evidence that transcriptional regulation is the complex behavior that emerges not solely from the individual components, but rather from their collective behavior, including competition and cooperation. Our framework describes individual regulatory components using generic action oriented descriptions of their biochemical interactions with a DNA sequence. All the possible actions are based on the current state of factors bound to the DNA. We developed a rule builder to automatically generate the complete set of biochemical interaction rules for any given DNA sequence. Off-the-shelf stochastic simulation engines can model the behavior of a system of rules and the resulting changes in the configuration of bound factors can be visualized. We compared our model to experimental data at well-studied loci in yeast, confirming that our model captures both the positional and temporal behavior of transcriptional regulation.
机译：我们提出了一个旨在捕获真核细胞中转录调节蛋白的位置和时间行为的建模框架。越来越多的证据表明，转录调控是一种复杂的行为，它不仅来自各个组成部分，而且还来自它们的集体行为，包括竞争与合作。我们的框架使用与DNA序列生化相互作用的通用作用导向描述描述了各个调控成分。所有可能的措施都是基于与DNA结合的因子的当前状态。我们开发了一个规则构建器，可以为任何给定的DNA序列自动生成完整的生化相互作用规则集。现成的随机模拟引擎可以对规则系统的行为进行建模，并且可以可视化绑定因子配置的结果变化。我们将我们的模型与酵母研究充分的基因座处的实验数据进行了比较，证实了我们的模型同时捕获了转录调控的位置和时间行为。

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