Del Mondo Géraldine, Eveillard Damien, Rusu Irena
Computational Biology Group- LINA, Université de Nantes, CNRS UMR 6241, Nantes, France.
Bioinformatics. 2009 Apr 1;25(7):926-32. doi: 10.1093/bioinformatics/btp083. Epub 2009 Feb 17.
Modules in biology appeared quickly as an accurate way for summarizing complex living systems by simple ones. Therefore, finding an appropriate relationship between modules extracted from a biological graph and protein complexes remains a crucial task. Recent studies successfully proposed various descriptions of protein interaction networks. These approaches succeed in showing modules within the network and how the modules interact. However, describing the interactions within the modules, i.e. intra-modular interactions, remains little analyzed despite its interest for understanding module functions.
We overcome this weakness by adding a complementary description to the already successful approaches: a hierarchical decomposition named homogeneous decomposition. This decomposition represents a natural refinement of previous analyses and details interactions within a module. We propose to illustrate these improvements by three practical cases. Among them, we decompose the yeast protein interaction network and show reachable biological insights that might be extracted from a complex large-scale network.
A program is at disposal under CeCILL license at: www.lina.univ-nantes.fr/combi/DH/Home.html.
Supplementary data are available at Bioinformatics online.
生物学中的模块作为一种通过简单系统总结复杂生命系统的准确方式迅速出现。因此，找到从生物图中提取的模块与蛋白质复合物之间的适当关系仍然是一项关键任务。最近的研究成功地提出了蛋白质相互作用网络的各种描述。这些方法成功地展示了网络中的模块以及模块之间的相互作用。然而，尽管模块内相互作用对于理解模块功能很有意义，但对其描述仍很少被分析。
我们通过在已成功的方法中添加一种补充描述来克服这一弱点：一种名为均匀分解的层次分解。这种分解是对先前分析的自然细化，并详细说明了模块内的相互作用。我们建议通过三个实际案例来说明这些改进。其中，我们分解了酵母蛋白质相互作用网络，并展示了可能从复杂的大规模网络中提取的可及生物学见解。
可在CeCILL许可下获取程序，网址为：www.lina.univ-nantes.fr/combi/DH/Home.html。
补充数据可在《生物信息学》在线获取。
