Mechanotransduction map: simulation model, molecular pathway, gene set
Mechanotransduction map: simulation model, molecular pathway, gene set
复制标题
DOI：
10.1093/bioinformatics/btu776
复制
发表时间：
2015-04-01
期刊：
影响因子：
5.8
通讯作者：
Nardini, Christine
中科院分区：
文献类型：
--
作者：
Dent, Jennifer E.;Devescovi, Valentina;Nardini, Christine
动机：机械转导-从机械输入输出生化信号的能力-与广谱分子事件的起始和进展有关。然而，机械转导的表征缺乏一些最基本的工具，例如，它很难被富集分析工具识别，我们也找不到任何途径表示。这极大地限制了计算测试和假设生成mechanotransduction生物相关性和参与疾病或生理mechanism.Results：我们在这里提出了一个mechanotransduction的分子地图，内置在CellDesigner保证最大的信息嵌入在一个紧凑的网络格式。为了验证地图的必要性，我们测试了它的冗余度与现有的途径相比，并估计其充分性，我们量化了它的能力，再现生物事件的动态模拟，使用信令Petri网。
Motivation: Mechanotransduction-the ability to output a biochemical signal from a mechanical input-is related to the initiation and progression of a broad spectrum of molecular events. Yet, the characterization of mechanotransduction lacks some of the most basic tools as, for instance, it can hardly be recognized by enrichment analysis tools, nor could we find any pathway representation. This greatly limits computational testing and hypothesis generation on mechanotransduction biological relevance and involvement in disease or physiological mechanisms.Results: We here present a molecular map of mechanotransduction, built in CellDesigner to warrant that maximum information is embedded in a compact network format. To validate the map's necessity we tested its redundancy in comparison with existing pathways, and to estimate its sufficiency, we quantified its ability to reproduce biological events with dynamic simulations, using Signaling Petri Networks.