Geryk Jan, Slanina Frantisek
Faculty of Science, Department of Philosophy and History of Sciences, Charles University, Vinicná 7, 128 44 Prague, Czech Republic.
Int J Data Min Bioinform. 2013;8(2):188-202. doi: 10.1504/ijdmb.2013.055500.
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E. coli. We introduce novel clustering algorithm and compare it with mainstream module detection method based on simulated annealing. Both methods identify the similar modular core. Slight but significant increase in modularity is observed after regulatory interactions addition. We also identify new functional modules in the combined network, which cannot be detected in the metabolic network only. Regulatory loops in the modules are the source of their autonomy, and allow us to hypothesise about module function.
我们研究了代谢网络与代表大肠杆菌中小代谢物对酶的直接调控的调控网络相结合时的模块化结构。我们引入了新颖的聚类算法，并将其与基于模拟退火的主流模块检测方法进行比较。两种方法都识别出了相似的模块化核心。在添加调控相互作用后，观察到模块化程度有轻微但显著的增加。我们还在组合网络中识别出了仅在代谢网络中无法检测到的新功能模块。模块中的调控环是其自主性的来源，并使我们能够对模块功能进行假设。
