Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China.
PLoS Comput Biol. 2024 Jan 30;20(1):e1011851. doi: 10.1371/journal.pcbi.1011851. eCollection 2024 Jan.
The unique expression patterns of circRNAs linked to the advancement and prognosis of cancer underscore their considerable potential as valuable biomarkers. Repurposing existing drugs for new indications can significantly reduce the cost of cancer treatment. Computational prediction of circRNA-cancer and drug-cancer relationships is crucial for precise cancer therapy. However, prior computational methods fail to analyze the interaction between circRNAs, drugs, and cancer at the systematic level. It is essential to propose a method that uncover more valuable information for achieving cancer-centered multi-association prediction. In this paper, we present a novel computational method, AutoEdge-CCP, to unveil cancer-associated circRNAs and drugs. We abstract the complex relationships between circRNAs, drugs, and cancer into a multi-source heterogeneous network. In this network, each molecule is represented by two types information, one is the intrinsic attribute information of molecular features, and the other is the link information explicitly modeled by autoGNN, which searches information from both intra-layer and inter-layer of message passing neural network. The significant performance on multi-scenario applications and case studies establishes AutoEdge-CCP as a potent and promising association prediction tool.
circRNA 与癌症进展和预后相关的独特表达模式,凸显了它们作为有价值的生物标志物的巨大潜力。重新利用现有药物用于新的适应症,可以显著降低癌症治疗的成本。circRNA-癌症和药物-癌症关系的计算预测对于精确的癌症治疗至关重要。然而,之前的计算方法未能在系统层面上分析 circRNAs、药物和癌症之间的相互作用。因此,提出一种方法来挖掘更多有价值的信息,以实现以癌症为中心的多关联预测,这一点至关重要。在本文中,我们提出了一种新的计算方法 AutoEdge-CCP,用于揭示与癌症相关的 circRNA 和药物。我们将 circRNA、药物和癌症之间的复杂关系抽象为一个多源异质网络。在这个网络中,每个分子都由两种类型的信息表示,一种是分子特征的内在属性信息,另一种是由 autoGNN 显式建模的链接信息,它从消息传递神经网络的内部层和外部层搜索信息。在多场景应用和案例研究中的显著性能,确立了 AutoEdge-CCP 作为一种强大且有前途的关联预测工具。