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Hither-CMI:基于混合多模态网络和通过图卷积网络的高阶邻域信息预测环状RNA-微小RNA相互作用

Hither-CMI: Prediction of circRNA-miRNA Interactions Based on a Hybrid Multimodal Network and Higher-Order Neighborhood Information via a Graph Convolutional Network.

作者信息

Jiang Chen, Wang Lei, Yu Chang-Qing, You Zhu-Hong, Wang Xin-Fei, Wei Meng-Meng, Shi Tai-Long, Liang Si-Zhe, Wang Deng-Wu

机构信息

School of Information Engineering, Xijing Univerity, Xi'an 710123, China.

Guangxi Academy of Science, Nanning 530007, China.

出版信息

J Chem Inf Model. 2025 Jan 13;65(1):446-459. doi: 10.1021/acs.jcim.4c01991. Epub 2024 Dec 17.

Abstract

Numerous studies show that circular RNA (circRNA) functions as a sponge for microRNA (miRNA), significantly regulating gene expression by interacting with miRNA, which in turn affects the progression of human diseases. Traditional experimental approaches for investigating circRNA-miRNA interactions (CMI) are both time-consuming and costly, making computational methods a valuable alternative. Hence, we propose a computational model for predicting CMI, leveraging a ybrid multmodal nework and igher-order nighborhood infomation (Hither-CMI). Specifically, Hither-CMI employs Multiple Kernel Learning (MKL) to integrate sequence, structure, and expression similarity networks of circRNA and miRNA, resulting in a hybrid multimodal network. Next, an enhanced Graph Convolutional Network (GCN) is utilized to combine the circRNA-miRNA hybrid multimodal network with the CMI association network, producing a hybrid higher-order embedding representation. Finally, the XGBoost classifier is applied for training and prediction. The Hither-CMI model achieved a predicted AUC value of 0.9134. In case studies, 25 out of the top 30 predicted CMI were confirmed by recent literature. These extensive experimental results further validate the effectiveness of Hither-CMI in predicting potential CMI, making it a promising prescreening tool for further biological research.

摘要

大量研究表明,环状RNA(circRNA)作为微小RNA(miRNA)的海绵,通过与miRNA相互作用显著调节基因表达,进而影响人类疾病的进展。传统的研究circRNA与miRNA相互作用(CMI)的实验方法既耗时又昂贵,这使得计算方法成为一种有价值的替代方案。因此,我们提出了一种用于预测CMI的计算模型,即利用混合多模态网络和高阶邻域信息(Hither-CMI)。具体而言,Hither-CMI采用多核学习(MKL)来整合circRNA和miRNA的序列、结构及表达相似性网络,从而得到一个混合多模态网络。接下来,使用增强型图卷积网络(GCN)将circRNA-miRNA混合多模态网络与CMI关联网络相结合,生成一个混合高阶嵌入表示。最后,应用XGBoost分类器进行训练和预测。Hither-CMI模型的预测AUC值达到了0.9134。在案例研究中,前30个预测的CMI中有25个得到了近期文献的证实。这些广泛的实验结果进一步验证了Hither-CMI在预测潜在CMI方面的有效性,使其成为进一步生物学研究的一个有前景的预筛选工具。

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