检索结果-南通市图书馆

Biased random walk with restart for essential proteins prediction

Chinese Physics B 2022年第11期31卷 638-648页

作者： Pengli Lu Yuntian Chen Teng Zhang Yonggang Liao School of Computer and Communication Lanzhou University of TechnologyLanzhou 730050China China Mobile Communications Group Gansu Co. Ltd.Lanzhou 730070China

Predicting essential proteins is crucial for discovering the process of cellular organization and *** propose biased random walk with restart algorithm for essential proteins prediction,called ***,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 *** address this problem,we redefine a novel transition probability matrix by integrating the gene express similarity and subcellular location *** particles can obtain biased transferring probabilities to perform random walk so as to further exploit biological properties embedded in the network ***,we use gene ontology(GO)terms score and subcellular score to calculate the initial probability vector of the random walk with ***,when the biased random walk with restart process reaches steady state,the protein importance score is *** order to demonstrate superiority of BRWR,we conduct experiments on the YHQ,BioGRID,Krogan and Gavin PPI *** results show that the method BRWR is superior to other state-of-the-art methods in essential proteins recognition ***,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%,***,BRWR is effective and reasonable.

关键词： PPI network essential proteins random walk with restart gene expression

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

AG-GATCN:A novel method for predicting essential proteins

引用

Chinese Physics B 2023年第5期32卷 737-745页

作者：杨培实卢鹏丽张腾 School of Computer and Communication Lanzhou University of TechnologyLanzhou 730050China

essential proteins play an important role in disease diagnosis and drug *** methods have been devoted to the essential protein prediction by using some kinds of biological ***,they either ignore the noise presented in the biological information itself or the noise generated during feature *** overcome these problems,in this paper,we propose a novel method for predicting essential proteins called attention gate-graph attention network and temporal convolutional network(AG-GATCN).In AG-GATCN method,we use improved temporal convolutional network(TCN)to extract features from gene expression *** address the noise in the gene expression sequence itself and the noise generated after the dilated causal convolution,we introduce attention mechanism and gating mechanism in *** addition,we use graph attention network(GAT)to extract protein–protein interaction(PPI)network features,in which we construct the feature matrix by introducing node2vec technique and 7 centrality metrics,and to solve the GAT oversmoothing problem,we introduce gated tanh unit(GTU)in ***,two types of features are integrated by us to predict essential *** with the existing methods for predicting essential proteins,the experimental results show that AG-GATCN achieves better performance.

关键词： complex networks essential proteins temporal convolutional network graph attention network gene expression

来源：

维普期刊数据库

同方期刊数据库评论

在线全文

学校读者我要写书评

暂无评论

Continuous and Discrete Similarity Coefficient for Identifying essential proteins Using Gene Expression Data

引用

Big Data Mining and Analytics 2023年第2期6卷 185-200页

作者： Jiancheng Zhong Zuohang Qu Ying Zhong Chao Tang Yi Pan College of Information Science and Engineering Hunan Normal UniversityChangsha 410081China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences ShenzhenGuangzhou 518055China

essential proteins play a vital role in biological processes,and the combination of gene expression profiles with Protein-Protein Interaction(PPI)networks can improve the identification of essential ***,gene expression data are prone to significant fluctuations due to noise interference in topological *** this work,we discretized gene expression data and used the discrete similarities of the gene expression spectrum to eliminate noise *** then proposed the Pearson Jaccard coefficient(PJC)that consisted of continuous and discrete similarities in the gene expression *** the graph theory as the basis,we fused the newly proposed similarity coefficient with the existing network topology prediction algorithm at each protein node to recognize essential *** strategy exhibited a high recognition rate and good *** validated the new similarity coefficient PJC on PPI datasets of Krogan,Gavin,and DIP of yeast species and evaluated the results by receiver operating characteristic analysis,jackknife analysis,top analysis,and accuracy *** with that of node-based network topology centrality and fusion biological information centrality methods,the new similarity coefficient PJC showed a significantly improved prediction performance for essential proteins in DC,IC,Eigenvector centrality,subgraph centrality,betweenness centrality,closeness centrality,NC,PeC,and *** also compared the PJC coefficient with other methods using the NF-PIN algorithm,which predicts proteins by constructing active PPI networks through dynamic gene *** experimental results proved that our newly proposed similarity coefficient PJC has superior advantages in predicting essential proteins.

关键词： Protein-Protein Interaction(PPI)network continuous and discrete similarity coefficient essential proteins

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Novel Scheme for essential proteins Identification Based on Improved Multicriteria Decision Making

引用

Journal of Shanghai Jiaotong university(Science) 2023年第4期28卷 418-431页

作者：卢鹏丽陈云天廖永刚 School of Computer and Communication Lanzhou University of TechnologyLanzhou 730050China China Mobile Communications Group Gansu Co. Ltd.Lanzhou 730070China

Identifying essential proteins from protein-protein interaction networks is important for studies onbiological evolution and new drug’s *** of the presented criteria for prioritizing essential proteinsonly focus on a certain attribute of the proteins in the network,which suffer from information *** order toovercome this problem,a relatively comprehensive and effective novel method for essential proteins identificationbased on improved multicriteria decision making(MCDM),called essential proteins identification-technique fororder preference by similarity to ideal solution(EPI-TOPSIS),is ***,considering different attributes ofproteins,we propose three methods from different aspects to evaluate the significance of the proteins:gene-degreecentrality(GDC)for gene expression sequence;subcellular-neighbor-degree centrality(SNDC)and subcellular-indegree centrality(SIDC)for subcellular location information and protein ***,betweenness centrality(BC)and these three methods are considered together as the multiple criteria of the decision-making *** hierarchy process is used to evaluate the weights of each criterion,and the essential proteins are prioritizedby an ideal solution of MCDM,i.e.,*** are conducted on YDIP,YMIPS,Krogan and *** results indicate that EPI-TOPSIS outperforms several state-of-the-art approaches for identifyingthe essential proteins through the performance measures.

关键词： protein-protein interaction network essential proteins multicriteria decision making(MCDM) biological information

来源：

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

欢迎您,

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

在线全文

在线全文

在线全文

请选择保存的检索档案：

请选择收藏分类：

通借通还

欢迎您,

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

在线全文

在线全文

在线全文

在线全文

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：