Identification of essential proteins is important for understanding cell survival and development, because even if only one of these proteins is missing, organisms cannot survive or develop. Since traditional methods ...
详细信息
Identification of essential proteins is important for understanding cell survival and development, because even if only one of these proteins is missing, organisms cannot survive or develop. Since traditional methods for identifying essential proteins based on biological experiments are costly and inefficient, more and more computational models are proposed for predicting essential proteins in recent years. In this paper, a novel computational model called BSPM is proposed, in which, an original PPI network will be built based on known protein-protein associations first, and then topology information of the original PPI network will be adopted to measure the similarities between proteins based on the simrank algorithm. Thereafter, a weighted PPI network can be obtained based on the similarities between proteins and the original PPI network. Finally, based on the weighted PPI network, the PageRank algorithm will be used to infer potential essential proteins. Moreover, in order to evaluate the performance of BSPM, we have compared the performance of BSPM with 14 classical prediction models in the field based on two different databases, and experimental results show that BSPM can achieve prediction accuracies of 92%, 81% and 76% out of the top 100, 200 and 300 candidate proteins separately, which not only are significantly better than those 14 competitive classical prediction models, but also means that BSPM can be used as an effective model for identifying essential proteins in the future.
Identifying essential proteins is important for not only understanding cellular activity but also detecting human disease genes. A series of centrality measures have been proposed to identify essential proteins based ...
详细信息
Identifying essential proteins is important for not only understanding cellular activity but also detecting human disease genes. A series of centrality measures have been proposed to identify essential proteins based on the protein-protein interaction (PPI) network. Although, existing studies have focused on the topological features of the PPI network and the intrinsic characteristics of biological attributes. it is still a big challenge to further improve the prediction accuracy of essential proteins. Moreover, there are substantial amounts of false-positive data in PPI networks;thus, a PPI network should be modelled as an uncertain network. How to identify essential proteins more accurately and conveniently has become a research hotspot. In this paper, we proposed a new essential protein discovery method called ETB-UPPI on uncertain PPI networks. The algorithm detects essential proteins by integrating topological features with biological information. Experimental results on four Saccharomyces cerevisiae datasets have shown that ETB-UPPI can not only improve the prediction accuracy but also outperform other prediction methods, including the most commonly-used centrality measures (DC, SC, BC, IC, EC, and NC), topology-based methods (LAC) and biological-data-integrating methods (PeC, WDC, UDONC, LBCC, TEGS, and RSG).
暂无评论