Identification of proliferative diabetic retinopathy-associated genes on the protein-protein interaction network by using heat diffusion algorithm
Identification of proliferative diabetic retinopathy-associated genes on the protein-protein interaction network by using heat diffusion algorithm
复制标题
利用热扩散算法识别蛋白质-蛋白质相互作用网络上的增殖性糖尿病视网膜病变相关基因
DOI：
10.1016/j.bbadis.2020.165794
复制
发表时间：
2020
影响因子：
6.2
通讯作者：
Xu Xun
中科院分区：
文献类型：
--
作者：
Zhang Jian;Zhang Meihua;Zhao Huijie;Xu Xun
糖尿病视网膜病变是糖尿病的常见并发症，可引起视网膜的致病性损伤。特别是增殖性糖尿病视网膜病变（PDR）状态可引起视网膜组织血管生成异常，并在晚期引发视网膜破坏。在临床上，PDR发生和发展过程中的症状相对难以识别。因此，对PDR发病机制的研究一直是各方关注的焦点。根据已发表的文献，遗传因素在PDR的发生和发展中起着不可替代的作用。尽管许多计算方法，如基于重启的最短路径和随机行走方法，已经应用于PDR潜在致病因素的筛选，但仍然广泛需要先进的计算方法，这些方法可能是先前计算方法的重要补充。在这项研究中，提出了一种新的计算方法来推断新的pdr相关基因。与以往的方法不同，本工作中使用的方法采用了不同的网络算法，即拉普拉斯热扩散算法。该算法应用于STRING数据库中报道的蛋白-蛋白相互作用网络。进行了三次筛选测试，以过滤最可能推断的基因。利用该方法共获取了26个基因。与前两次预测相比，大多数鉴定出的基因都是新的，只有一个基因是共享的。一些推断基因如csf3、COL18A1、CXCR2、CCR1、FGF23、CXCL11和il13与PDR的发病有关。
Diabetic retinopathy is a common complication of diabetes mellitus that causes pathogenic damage to the retina. Particularly, the proliferative diabetic retinopathy (PDR) state can cause abnormal angiogenesis in the retina tissues and trigger the retina destruction in advanced stage. In the clinic, the symptoms during the initiation and progression of PDR are relatively unrecognizable. Therefore, various studies have focused on the pathogenesis of PDR. According to published literature, genetic contributions play an irreplaceable role in the initiation and progression of PDR. Although many computational methods, such as shortest path- and random walk with restart-based methods, have been applied in screening the potential pathogenic factors of PDR, advanced computational methods, which may provide essential supplements for previous ones, are still widely needed. In this study, a novel computational method was presented to infer novel PDR-associated genes. Different from previous methods, the method used in this work employed a different network algorithm, that is, the Laplacian heat diffusion algorithm. This algorithm was applied on the protein–protein interaction network reported in the STRING database. Three screening tests were performed to filter the most likely inferred genes. A total of 26 genes were accessed using the proposed method. Compared with the two previous predictions, most of the identified genes were novel, and only one gene was shared. Several inferred genes, such asCSF3,COL18A1,CXCR2,CCR1,FGF23,CXCL11, andIL13, were related to the pathogenesis of PDR.