School of Life Sciences, Shanghai University, 200444, Shanghai, People's Republic of China.
College of Information Engineering, Shanghai Maritime University, 201306, Shanghai, People's Republic of China.
Gene Ther. 2019 Dec;26(12):465-478. doi: 10.1038/s41434-019-0099-y. Epub 2019 Aug 27.
Oral cancer (OC) is one of the most common cancers threatening human lives. However, OC pathogenesis has yet to be fully uncovered, and thus designing effective treatments remains difficult. Identifying genes related to OC is an important way for achieving this purpose. In this study, we proposed three computational models for inferring novel OC-related genes. In contrast to previously proposed computational methods, which lacked the learning procedures, each proposed model adopted a one-class learning algorithm, which can provide a deep insight into features of validated OC-related genes. A network embedding algorithm (i.e., node2vec) was applied to the protein-protein interaction network to produce the representation of genes. The features of the OC-related genes were used in the training of the one-class algorithm, and the performance of the final inferring model was improved through a feature selection procedure. Then, candidate genes were produced by applying the trained inferring model to other genes. Three tests were performed to screen out the important candidate genes. Accordingly, we obtained three inferred gene sets, any two of which were different. The inferred genes were also different from previous reported genes and some of them have been included in the public Oral Cancer Gene Database. Finally, we analyzed several inferred genes to confirm whether they are novel OC-related genes.
口腔癌 (OC) 是威胁人类生命的最常见癌症之一。然而，OC 的发病机制尚未完全揭示，因此设计有效的治疗方法仍然很困难。鉴定与 OC 相关的基因是实现这一目标的重要途径。在这项研究中，我们提出了三种用于推断新型 OC 相关基因的计算模型。与以前提出的缺乏学习过程的计算方法不同，每个提出的模型都采用了一类学习算法，可以深入了解验证的 OC 相关基因的特征。网络嵌入算法（即 node2vec）被应用于蛋白质-蛋白质相互作用网络，以产生基因的表示。OC 相关基因的特征被用于一类算法的训练中，通过特征选择过程提高了最终推断模型的性能。然后，通过应用训练有素的推断模型将候选基因应用于其他基因。进行了三项测试以筛选出重要的候选基因。因此，我们获得了三个推断的基因集，其中任意两个都不同。推断的基因也与以前报道的基因不同，其中一些已包含在公共的口腔癌基因数据库中。最后，我们分析了几个推断的基因，以确认它们是否是新型 OC 相关基因。
