An Arabidopsis gene network based on the graphical Gaussian model
An Arabidopsis gene network based on the graphical Gaussian model
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DOI：
10.1101/gr.6911207
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发表时间：
2007-11-01
期刊：
影响因子：
7
通讯作者：
Bohnert, Hans J.
中科院分区：
文献类型：
--
作者：
Ma, Shisong;Gong, Qingqiu;Bohnert, Hans J.
我们描述了一个基因网络的拟南芥转录组的基础上修改的图形高斯模型（GGM）。通过偏相关（pcor），GGM推断基因对之间的协同调节模式的条件下，其他基因的行为。正则化GGM一次计算约2000个输入基因中基因对之间的pcor。正则化GGM加上基因的迭代随机采样扩展到覆盖拟南芥基因组（22，266个基因）的网络中。这导致了6760个基因（节点）之间的18，625个相互作用（边缘）的网络，具有高置信度和代表所有可能边缘的约0.01%的连接。当查询选定的基因，局部相关的子网络主要与代谢功能，压力反应出现。生物化学途径，细胞壁代谢和冷反应的网络的例子。GGM显示已知的共调节途径的子网络，并添加新的组件已知的边缘。最后，该网络协调了在全基因组水平上连接的拓扑结构中的各个子网络，并提供了一个总体框架，可以指导未来对植物代谢和胁迫反应的研究。包括网络模型。
We describe a gene network for the Arabidopsis thaliana transcriptome based on a modified graphical Gaussian model (GGM). Through partial correlation (pcor), GGM infers coregulation patterns between gene pairs conditional on the behavior of other genes. Regularized GGM calculated pcor between gene pairs among -2000 input genes at a time. Regularized GGM coupled with iterative random samplings of genes was expanded into a network that covered the Arabidopsis genome (22,266 genes). This resulted in a network of 18,625 interactions (edges) among 6760 genes (nodes) with high confidence and connections representing -0.01% of all possible edges. When queried for selected genes, locally coherent subnetworks mainly related to metabolic functions, and stress responses emerged. Examples of networks for biochemical pathways, cell wall metabolism, and cold responses are presented. GGM displayed known coregulation pathways as subnetworks and added novel components to known edges. Finally, the network reconciled individual subnetworks in a topology joined at the whole-genome level and provided a general framework that can instruct future studies on plant metabolism and stress responses. The network model is included.