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基于多标记学习预测药物-靶标相互作用 被引量:4
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作者 彭利红 刘海燕 +2 位作者 任日丽 马俊 王建芬 《计算机工程与应用》 CSCD 北大核心 2017年第15期260-265,共6页
对药物-靶标关联进行了研究,提出基于弱标记和多信息融合的药物-靶标相互作用预测方法 PDML。通过与其他方法对比和数据库检索验证评估PDML模型的性能:与Yamanishi提出的方法、RLSMDA、Lap RLS及Net CBP相比,除在核受体数据集中该方法在... 对药物-靶标关联进行了研究,提出基于弱标记和多信息融合的药物-靶标相互作用预测方法 PDML。通过与其他方法对比和数据库检索验证评估PDML模型的性能:与Yamanishi提出的方法、RLSMDA、Lap RLS及Net CBP相比,除在核受体数据集中该方法在AUC上的性能比Lap RLS略有降低之外,模型在敏感性、特异性、AUC和AUPR上的性能均优于其他四种方法;提取前5个预测分值最高的药物-靶标对,这些药物-靶标对能通过检索Drug Bank、Super Target和KEGG数据库而得到验证。 展开更多
关键词 药物-靶标相互作用 多标记学习 多信息融合 药物-靶标相互作用网络 药物相似性
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一种多信息融合的药物-靶标关联预测算法 被引量:3
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作者 彭利红 李泽军 +1 位作者 陈敏 任日丽 《计算机工程》 CAS CSCD 北大核心 2016年第6期218-223,229,共7页
在药物结构相似性和靶标序列相似性的基础上,结合药物-靶标相互作用网络信息,考虑分类器和数据集合分布的复杂性,提出一种半监督学习算法预测药物与靶标之间的关联。实验结果表明,该算法的预测性能较DBSI,KBMF2K等算法有所提高。对其预... 在药物结构相似性和靶标序列相似性的基础上,结合药物-靶标相互作用网络信息,考虑分类器和数据集合分布的复杂性,提出一种半监督学习算法预测药物与靶标之间的关联。实验结果表明,该算法的预测性能较DBSI,KBMF2K等算法有所提高。对其预测到的药物-靶标相互作用数据进行打分并排序,从中提取前30%的数据,其中有部分相互作用可在KEGG,Drug Bank,Super Target和Ch EMBL数据库中得到验证。 展开更多
关键词 多信息融合 半监督学习 药物-靶标相互作用网络 药物相似性 靶标相似性
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基于生物网络探讨防治冠心病药物作用机制 被引量:5
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作者 张燕玲 黄明峰 乔延江 《中国中药杂志》 CAS CSCD 北大核心 2013年第16期2721-2727,共7页
该文以冠心病疾病相关基因和靶点以及防治冠心病药物作用靶点为研究对象,分别构建冠心病疾病网络和防治冠心病药物作用网络,并对网络的度分布、特征路径长度、连通情况和异质性等网络拓扑特征参数进行分析,验证了网络的可靠性;在此基础... 该文以冠心病疾病相关基因和靶点以及防治冠心病药物作用靶点为研究对象,分别构建冠心病疾病网络和防治冠心病药物作用网络,并对网络的度分布、特征路径长度、连通情况和异质性等网络拓扑特征参数进行分析,验证了网络的可靠性;在此基础上对2个网络取Intersection计算,对二者的交集子网络进行药物作用机制解析。所构建的冠心病疾病网络含有15 221个节点和31 177条边、防治冠心病药物作用网络含有15 073个节点和32 376条边,2个网络的拓扑特征参数表明均具有无标度和小世界的整体结构特性。本文以交集子网络中降钙素基因相关肽和IL-6激活JAK/STAT 2个反应途径为例,探讨阐释了药物防治冠心病的间接作用机制。研究结果表明将疾病网络与药物作用网络相互结合的生物网络分析方法有助于进一步深入认识药物治疗的作用机制,对于疾病的预防和治疗具有重要价值。 展开更多
关键词 冠心病 疾病网络 药物作用网络 网络特征 作用机制
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基于多标记学习预测药物-靶标相互作用
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作者 彭利红 刘海燕 +2 位作者 任日丽 马俊 王建芬 《长沙医学院学报》 2018年第1期23-28,共6页
对药物-靶标关联进行了研究,提出基于弱标记和多信息融合的药物-靶标相互作用预测方法PDML.通过与其他方法对比和数据库检索验证评估PDML模型的性能:与Yamanishi提出的方法、RLSMDA、LapRLS及NetCBP相比,除在核受体数据集中该方法在AUC... 对药物-靶标关联进行了研究,提出基于弱标记和多信息融合的药物-靶标相互作用预测方法PDML.通过与其他方法对比和数据库检索验证评估PDML模型的性能:与Yamanishi提出的方法、RLSMDA、LapRLS及NetCBP相比,除在核受体数据集中该方法在AUC上的性能比LapRLS略有降低之外,模型在敏感性,特异性、AUC和AUPR上的性能均优于其他四种方法;提取前5个预测分值最高的药物-靶标对,这些药物-靶标对能通过检索DrugBank、SuperTarget和KEGG数据库而得到验证。 展开更多
关键词 药物-靶标相互作用 多标记学习 多信息融合 药物-靶标相互作用网络 药物相似性
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Exploring the Action Mechanism of Yadanzi(Brucea javanica)in the Treatment of Glioblastoma Based on Bioinformatics and Network Pharmacology
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作者 Wenyu Zhao Fuchun Si 《Chinese Medicine and Natural Products》 2022年第2期67-76,共10页
ObjectiveThe aim of the study is to explore the molecular mechanism of Yadanzi(Brucea javanica)in the treatment of glioblastoma(GBM)by using the methods of bioinformatics and network pharmacology.Methods The Tradition... ObjectiveThe aim of the study is to explore the molecular mechanism of Yadanzi(Brucea javanica)in the treatment of glioblastoma(GBM)by using the methods of bioinformatics and network pharmacology.Methods The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)and literature retrieval method were applied to obtain the active ingredients of Yadanzi(Brucea javanica),and to predict the relevant targets of the active ingredients.The GBM-related targets were retrieved and screened through the Gene Expression Profling Interactive Analysis(GEPIA)database,and mapped to each other with the targets of the components of Yadanzi(Brucea javanica)to obtain the intersection targets.The GBM differentially expressed gene targets were imported into the String database to obtain the protein interaction relationship,the Cytoscape software was used to draw the protein interaction network,the Cytobba and MCODE plug-ins were used to screen the core genes and important protein interaction modules,and the GEPIA database was applied to make survival analysis of the core genes.The network map of“active ingredients-targets”was constructed through the Cytoscape 3.6.1 software.Gene Ontology(GO)biological function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)signaling pathway enrichment analysis for GBM differentially expressed genes were performed through the DAVID database.ResultsThrough TCMSP and literature retrieval,23 potential active ingredients and 129 related targets were obtained from Yadanzi(Brucea javanica).In the GEPIA database,247 GBM differentially expressed genes were screened,including 113 upregulated genes and 134 downregulated genes.After mapping with the targets related to the active ingredients of Yadanzi(Brucea javanica),six intersection targets were obtained,that is,the potential action targets of Yadanzi(Brucea javanica)in treating GBM,including MMP2,HMOX1,BIRC5,EGFR,CCNB2,and TOP2A.Cytoscape software was applied to build an“active ingredient-action target”network.Two active ingredients and five action targets of β-sitosterol(BS)and luteolin were found,and the targets were mainly concentrated in BS.It was found by KEGG pathway enrichment analysis that GBM differentially expressed genes were mainly involved in signaling pathways related to Staphylococcus aureus infection,phagosome formation,tuberculosis and systemic lupus erythematosus and other infectious and autoimmune diseases.It was found by GO enrichment analysis that the GBM differentially expressed genes mainly involved such biological processes(BP)as the processing and presentation of exogenous antigenic peptides and polysaccharide antigens through MHC Il molecules,y-interferon-mediated signaling pathways,extracellular matrix composition,and chemical synapses transmission;it involved cellular components such as cell junctions,axon terminal buttons,extracellular space,vesicle membranes for endocytosis,and MHC Il protein complexes;molecular functions such as calcium-mediated ionic protein binding,MHC Il molecular receptor activity,immunoglobulin binding,and phospholipase inhibitor activity were also involved.Survival analysis was conducted by GEPIA on the top 37 core targets in degree value,and a total of five genes related to GBM prognosis were obtained.Among them,FN1 and MMP2 were highly expressed while GABRD(v-aminobutyric acid A receptor delta subunit),RBFOX1,and SLC6A7 were expressed at a low level in cancer patients.Conclusion The pathogenesis of GBM is closely related to the human immune system,and BS and luteolin may be the main material basis of Yadanzi(Brucea javanica)for the treatment of GBM and the improvement of prognosis.The molecular mechanism may be related to the physical barrier formed by destroying the tumor cell stromal 68 Treatment of Glioblastoma Based on Bioinformatics and Network Pharmacology Zhao,Si.molecules and its involvement in tumor immune response. 展开更多
关键词 Yadanzi(Brucea javanica) GLIOBLASTOMA BIOINFORMATICS network pharmacology action mechanism
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A Study on the Basic Drugs and Points for Point Application in Summer to Treat the Diseases with Attacks in Winter 被引量:1
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作者 房繄恭 周雪忠 +2 位作者 刘保延 王永炎 段树民 《Journal of Traditional Chinese Medicine》 SCIE CAS CSCD 2010年第3期180-184,共5页
Objective: To study the basic prescriptions of drugs and points for point application in summer to treat the diseases with attacks in winter and the law governing their compatibility. Methods: A database was set up by... Objective: To study the basic prescriptions of drugs and points for point application in summer to treat the diseases with attacks in winter and the law governing their compatibility. Methods: A database was set up by collecting and sorting out the relevant literature, and the analysis was made with the complex network. Results: It was found that Bai Jie Zi (白芥子 Semen Sinapis Albae), Xi Xin (细辛 Herba Asari), Gan Sui (甘遂 Radix Euphorbiae Kansui) and Yan Hu Suo (延胡索 Rhizoma Corydalis) were used as the basic prescriptions of drugs, Feishu (BL 13), Dazhui (GV 14) and Shanzhong (CV 17) were selected as the basic prescription of points. Conclusion: The knowledge obtained from the complex networks on the basic prescriptions of drugs and points for point-application in summer to treat diseases with attacks in winter can provide a data support for working out operation norms and carrying on verification research. 展开更多
关键词 winter-disease-treated-in-summer acupoint application therapy literature study complicated network analysis herbal compatibility acupoint compatibility
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