Li Jie, Wang Bingbo, Ma Xiujuan
School of Computer Science and Technology, Xidian University, Xi'an 710119, China.
Entropy (Basel). 2024 Jul 27;26(8):640. doi: 10.3390/e26080640.
The emergence of cancers involves numerous coding and non-coding genes. Understanding the contribution of non-coding RNAs (ncRNAs) to the cancer neighborhood is crucial for interpreting the interaction between molecular markers of cancer. However, there is a lack of systematic studies on the involvement of ncRNAs in the cancer neighborhood. In this paper, we construct an interaction network which encompasses multiple genes. We focus on the fundamental topological indicator, namely connectivity, and evaluate its performance when applied to cancer-affected genes using statistical indices. Our findings reveal that ncRNAs significantly enhance the connectivity of affected genes and mediate the inclusion of more genes in the cancer module. To further explore the role of ncRNAs in the network, we propose a connectivity-based method which leverages the bridging function of ncRNAs across cancer-affected genes and reveals the non-coding RNAs extended omnigenic module (NeOModule). Topologically, this module promotes the formation of cancer patterns involving ncRNAs. Biologically, it is enriched with cancer pathways and treatment targets, providing valuable insights into disease relationships.
癌症的发生涉及众多编码基因和非编码基因。了解非编码RNA（ncRNA）对癌症邻域的作用对于解释癌症分子标志物之间的相互作用至关重要。然而，目前缺乏关于ncRNA参与癌症邻域的系统性研究。在本文中，我们构建了一个包含多个基因的相互作用网络。我们聚焦于基本的拓扑指标，即连通性，并使用统计指标评估其应用于癌症相关基因时的性能。我们的研究结果表明，ncRNA显著增强了相关基因的连通性，并介导更多基因纳入癌症模块。为了进一步探究ncRNA在网络中的作用，我们提出了一种基于连通性的方法，该方法利用ncRNA在癌症相关基因间的桥梁功能，揭示了非编码RNA扩展全基因模块（NeOModule）。在拓扑结构上，该模块促进了涉及ncRNA的癌症模式的形成。在生物学层面，它富含癌症通路和治疗靶点，为疾病关系提供了有价值的见解。
