Kosmidis Kosmas, Hütt Marc-Thorsten
Physics Department, Aristotle University of Thessaloniki, 54124, Panepistimioupolis, Greece.
PharmaInformatics Unit, Research Center ATHENA, Athens, Greece.
Eur Phys J E Soft Matter. 2019 Mar 20;42(3):30. doi: 10.1140/epje/i2019-11794-x.
Usually complex networks are studied as graphs consisting of nodes whose spatial arrangement is of no significance. Several real biological networks are, however, embedded in space. In this paper we study the transcription regulatory network (TRN) of E. coli as a spatially embedded network. The embedding space of this network is the circular E. coli chromosome, i.e. it is practically one dimensional. However, the TRN itself is a high-dimensional network due to the existence of an adequate number of long-range connections. We find that nodes in short topological distance l = 1, 2 tend, on average, to be in shorter spatial distances r indicating an abundance of short-range connections as well. Community analysis of the TRN reveals the interesting fact that highly interconnected subnets consist of nodes that tend to be in spatial proximity on the circular chromosome. We also find indications that for certain transcriptional aspects of the E. coli it is advantageous to treat the circular genome as two line segments starting from the OriC and ending to Ter.
通常，复杂网络被当作由节点组成的图来研究，这些节点的空间排列并无意义。然而，一些实际的生物网络是嵌入在空间中的。在本文中，我们将大肠杆菌的转录调控网络（TRN）作为一个空间嵌入网络来研究。该网络的嵌入空间是环状的大肠杆菌染色体，即实际上是一维的。然而，由于存在足够数量的长程连接，TRN本身是一个高维网络。我们发现，拓扑距离短（l = 1, 2）的节点平均而言在空间距离r上也较短，这表明也存在大量的短程连接。对TRN的群落分析揭示了一个有趣的事实，即高度互联的子网由在环状染色体上倾向于空间邻近的节点组成。我们还发现有迹象表明，对于大肠杆菌的某些转录方面，将环状基因组视为从OriC开始并终止于Ter的两条线段是有利的。
