Biased random walk with restart for essential proteins prediction  

作　　者：Pengli Lu Yuntian Chen Teng Zhang Yonggang Liao 卢鹏丽;陈云天;张腾;廖永刚(School of Computer and Communication,Lanzhou University of Technology,Lanzhou 730050,China;China Mobile Communications Group Gansu Co.,Ltd.,Lanzhou 730070,China)

机构地区：[1]School of Computer and Communication,Lanzhou University of Technology,Lanzhou 730050,China [2]China Mobile Communications Group Gansu Co.,Ltd.,Lanzhou 730070,China

出　　处：《Chinese Physics B》2022年第11期638-648,共11页中国物理B（英文版）

基　　金：Project supported by the National Natural Science Foundation of China(Grant Nos.11861045 and 62162040)。

摘　　要：Predicting essential proteins is crucial for discovering the process of cellular organization and viability.We propose biased random walk with restart algorithm for essential proteins prediction,called BRWR.Firstly,the common process of practice walk often sets the probability of particles transferring to adjacent nodes to be equal,neglecting the influence of the similarity structure on the transition probability.To address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location similarity.The particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network structure.Secondly,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with restart.Finally,when the biased random walk with restart process reaches steady state,the protein importance score is obtained.In order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI networks.The results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition performance.Especially,compared with the contrast methods,the improvements of BRWR in terms of the ACC results range in 1.4%–5.7%,1.3%–11.9%,2.4%–8.8%,and 0.8%–14.2%,respectively.Therefore,BRWR is effective and reasonable.

关 键 词：PPI network essential proteins random walk with restart gene expression 

分 类 号：O469[理学—凝聚态物理] O211.6[理学—电子物理学]