This paper introduces a new pattern, called interdependent patterns consisting of genes that are closely interdependent in the information transmission process on protein-protein interaction (PPI) networks. Firstly, information flow starts to broadcast from activated genes to any other genes through the shortest paths, in which information is processed, and retransmitted by the genes adhering to the paths. In the process, some genes are highly interdependent, called interdependent genes, i.e., the failure of one of them will trigger a cascading failure of some other of them. Then, for identifying interdependent patterns, we introduce a gene interdependent network (GIN), in which two genes are connected by a link if they are interdependent, and one interdependent pattern corresponds to a densely connected subnetwork in the GIN. Finally, we extract interdependent patterns in the GIN by the modularity optimization method. The results show that interdependent patterns are less likely to be the modular structures in PPI networks, i.e., the pairs of interdependent genes tend not to interact directly in PPI networks, and the genes without direct interactions are also enriched with biological significance.

中文翻译：

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蛋白质-蛋白质相互作用网络中的相互依赖模式


本文介绍了一种新的模式，称为相互依赖模式，由在蛋白质-蛋白质相互作用（PPI）网络上的信息传递过程中紧密相互依赖的基因组成。首先，信息流开始从激活的基因通过最短路径广播到任何其他基因，其中信息被处理，并由附着在路径上的基因重新传输。在这个过程中，一些基因是高度相互依赖的，称为相互依赖基因，即其中一个基因的失败将引发其他一些基因的级联失败。然后，为了识别相互依赖模式，我们引入了一种基因相互依赖网络（GIN），其中两个基因如果相互依赖则通过链接连接，并且一个相互依赖模式对应于 GIN 中的密集连接的子网络。最后，我们通过模块化优化方法提取 GIN 中的相互依赖模式。结果表明，相互依赖的模式不太可能是PPI网络中的模块化结构，即相互依赖的基因对在PPI网络中往往不直接相互作用，并且没有直接相互作用的基因也富含生物学意义。