Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks.
Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks.
复制标题
重新检查蛋白质亚细胞定位相互作用网络范围内的中心性-致死性规则
DOI：
10.1371/journal.pone.0130743
复制
发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Pan Y
中科院分区：
文献类型：
--
作者：
Peng X;Wang J;Wang J;Wu FX;Pan Y
必需蛋白是生物体维持生命活动所必需的，在病理学、合成生物学和药物设计研究中发挥着重要作用。因此，除了实验方法外，还提出了许多计算方法来鉴定必需蛋白质。基于中心性-致死性原则，采用多种中心性方法预测蛋白-蛋白相互作用网络（PIN）中的必需蛋白。然而，忽略了蛋白质-蛋白质相互作用的时间和空间特征，通过中心性方法计算的中心性分数不足以有效地测量PIN中蛋白质的重要性。此外，许多方法过度拟合一个物种的必需蛋白质特征，可能对其他物种表现不佳。在本文中，我们证明了在蛋白质亚细胞定位相互作用网络（PSLINs）中也存在中心性-致死性规则。为此，提出了一种基于必需蛋白定位特异性（Localization Specificity for Essential protein Detection， LSED）的方法，该方法可以与任何中心性方法相结合，通过考虑蛋白质在其中发挥作用的PSLINs来计算改进的中心性分数。在本研究中，LSED分别与8种中心性方法相结合，基于酿酒酵母（Saccharomyces cerevisiae）、智人（Homo sapiens）、小家鼠（Mus musus）和黑腹果蝇（Drosophila melanogaster） 4种物种的pslin计算蛋白质的定位特异性中心性评分（locationspecific centrality Scores, LCSs）。与从全局pin中测量到的具有高中心性得分的蛋白质相比，从PSLINs中测量到的具有高lcs的蛋白质是必需的。这表明从pslin中测量的高lcs的蛋白质更可能是必需的，并且LSED可以提高中心性方法的性能。此外，LSED为识别不同物种的必需蛋白提供了广泛适用的预测模型。
Essential proteins are indispensable for living organisms to maintain life activities and play important roles in the studies of pathology, synthetic biology, and drug design. Therefore, besides experiment methods, many computational methods are proposed to identify essential proteins. Based on the centrality-lethality rule, various centrality methods are employed to predict essential proteins in a Protein-protein Interaction Network (PIN). However, neglecting the temporal and spatial features of protein-protein interactions, the centrality scores calculated by centrality methods are not effective enough for measuring the essentiality of proteins in a PIN. Moreover, many methods, which overfit with the features of essential proteins for one species, may perform poor for other species. In this paper, we demonstrate that the centrality-lethality rule also exists in Protein Subcellular Localization Interaction Networks (PSLINs). To do this, a method based on Localization Specificity for Essential protein Detection (LSED), was proposed, which can be combined with any centrality method for calculating the improved centrality scores by taking into consideration PSLINs in which proteins play their roles. In this study, LSED was combined with eight centrality methods separately to calculate Localization-specific Centrality Scores (LCSs) for proteins based on the PSLINs of four species (Saccharomyces cerevisiae, Homo sapiens, Mus musculus and Drosophila melanogaster). Compared to the proteins with high centrality scores measured from the global PINs, more proteins with high LCSs measured from PSLINs are essential. It indicates that proteins with high LCSs measured from PSLINs are more likely to be essential and the performance of centrality methods can be improved by LSED. Furthermore, LSED provides a wide applicable prediction model to identify essential proteins for different species.
登录
查看更多内容
影响因子：
4.4
作者：
Estrada, Ernesto
通讯作者：
Estrada, Ernesto
影响因子：
56.9
作者：
de Lichtenberg, U;Jensen, LJ;Bork, P
通讯作者：
Bork, P
影响因子：
64.8
作者：
Jeong, H;Mason, SP;Oltvai, ZN
通讯作者：
Oltvai, ZN
影响因子：
46.9
作者：
Matsuyama, Akihisa;Arai, Ritsuko;Yoshida, Minoru
通讯作者：
Yoshida, Minoru
影响因子：
4.4
作者：
BONACICH, P
通讯作者：
BONACICH, P