Rizi Abbas Karimi, Zamani Mina, Shirazi Amirhossein, Jafari G Reza, Kertész János
Physics Department, Shahid Beheshti University, Tehran, Iran.
Department of Network and Data Science, Central European University, Budapest, Hungary.
Front Physiol. 2021 Jan 20;11:573732. doi: 10.3389/fphys.2020.573732. eCollection 2020.
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex network structures in cells, and such structures are expected to be different for normal and cancerous cells. To study these differences, we have investigated the Gene Regulatory Network (GRN) of cells as inferred from RNA-sequencing data. The GRN is a signed weighted network corresponding to the inductive or inhibitory interactions. Here we focus on a particular of motifs in the GRN, the triangles, which are imbalanced if the number of negative interactions is odd. By studying the stability of imbalanced triangles in the GRN, we show that the network of cancerous cells has fewer imbalanced triangles compared to normal cells. Moreover, in the normal cells, imbalanced triangles are isolated from the main part of the network, while such motifs are part of the network's giant component in cancerous cells. Our result demonstrates that due to genes' collective behavior the structure of the complex networks is different in cancerous cells from those in normal ones.
基因通过不同的调控效应相互通信，这导致细胞中出现复杂的网络结构，并且这种结构在正常细胞和癌细胞中预计会有所不同。为了研究这些差异，我们从RNA测序数据推断出细胞的基因调控网络（GRN）进行了研究。GRN是一个对应于诱导或抑制相互作用的带符号加权网络。在这里，我们专注于GRN中的一种特定基序，即三角形，如果负相互作用的数量为奇数，则这些三角形是不平衡的。通过研究GRN中不平衡三角形的稳定性，我们发现与正常细胞相比，癌细胞网络中的不平衡三角形较少。此外，在正常细胞中，不平衡三角形与网络的主要部分隔离，而在癌细胞中，这些基序是网络巨大组件的一部分。我们的结果表明，由于基因的集体行为，癌细胞中复杂网络的结构与正常细胞中的不同。
