Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
复制标题
DOI：
10.1093/nar/gkm769
复制
发表时间：
2007-11-01
影响因子：
14.9
通讯作者：
Zhao, Quanyu
中科院分区：
文献类型：
--
作者：
Kurata, Hiroyuki;Inoue, Kentaro;Zhao, Quanyu
生化网络图有助于理解一系列生化反应如何在细胞内产生特定功能的机制。我们开发了一种新的、在计算上可行的符号，它能够从现象学事件的域级反应中绘制出宽分辨率的地图，并将其实现为CADLIVE(计算机辅助生命系统设计)的扩展图形用户界面网络构造器。新的符号表示蛋白质和RNA的结构域扩展，虚拟反应和负责说明基于领域的相互作用的节点，以及将真实复杂节点与虚拟节点链接起来以说明真实复合体的确切组件的内部链接。还提出了一个模块化的盒子，将相关的反应打包为一个模块或一个子网络，这使CADLIVE能够在分层的模块化体系结构中绘制生化图。此外，我们开发了一个针对虚拟基因敲除突变体的路径搜索模块，作为CADLIVE的内置应用程序。这个模块以与分子遗传学相同的方式分析基因功能，模拟突变表型的变化或确认网络图的有效性。新提出的扩展CADLIVE用于计算模拟和分析是可行的。
Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents Domain expansion for proteins and RNAs, Virtual reaction and nodes that are responsible for illustrating domain-based interaction and InnerLink that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork, which gives CADLIVE a capability to draw biochemical maps in a hierarchical modular architecture. Furthermore, we developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map. The extended CADLIVE with the newly proposed notation is demonstrated to be feasible for computational simulation and analysis.