GeneNet: a gene network database and its automated visualization
GeneNet: a gene network database and its automated visualization
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DOI：
10.1093/bioinformatics/14.6.529
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发表时间：
1998-01-01
期刊：
影响因子：
5.8
通讯作者：
Kolchanov, NA
中科院分区：
文献类型：
--
作者：
Kolpakov, FA;Ananko, EA;Kolchanov, NA
动机：提供生理过程调节的基因网络是生物体的基本特征。关于基因表达调控和信号转导途径的信息正在迅速增加。然而，这些信息很难正式化和系统化。需要基于形式化描述的基因网络自动可视化的方法和手段。结果：开发了面向对象的基因网络数据库GeneNet及其自动可视化软件。提出了基因网络形式化描述的主要原则。提供抗病毒应答和红细胞生成作为示例以显示这是如何实现的。用Java编写的GeneNet图形用户界面提供了基因网络图的自动生成，并允许通过互联网可视化和探索GeneNet数据库。过滤器系统允许选择网络的特定组件进行可视化。
Motivation: Gene networks that provide the regulation of physiological processes are the basic feature of organisms. Information regarding the regulation of gene expression and signal transduction pathways is increasing rapidly. However, the information is hard to formalize and systematize. Ways and means for automated visualization of the gene networks based on their formalized description are needed.Results: The object-oriented database GeneNet and the software for its automated visualization have been developed. The main principles of a formalized description of the gene network have been worked out. Antiviral response and erythropoiesis are provided as examples to show how this is achieved. The GeneNet graphical user interface written in Java provides automated generation of the gene network diagrams and allows visualization and exploration of the GeneNet database through the Internet. A system of filters allows the selection of particular components of the network for visualization.