麦冬是重要的滋阴药,有养阴生津、清心除烦的功效,并具有多种化学成分和药理作用,在临床应用十分广泛。科学知识图谱是可以定量、客观地展示学科研究的发展前沿和方向的有效工具。该研究搜集Web of Science(WoS)及中国知网(CNKI)与麦冬...麦冬是重要的滋阴药,有养阴生津、清心除烦的功效,并具有多种化学成分和药理作用,在临床应用十分广泛。科学知识图谱是可以定量、客观地展示学科研究的发展前沿和方向的有效工具。该研究搜集Web of Science(WoS)及中国知网(CNKI)与麦冬相关的中医药研究文献,采用科学计量学软件CiteSpace对文献中涉及的研究机构、期刊和关键词进行可视化分析,构建麦冬相关研究的共现网络,利用Cytoscape 3.8.2绘制麦冬-疾病-靶点网络图谱。并针对中、英文文献研究热点进行内容分析,讨论当前研究热点,总结麦冬研究中存在的不足,探讨其发展趋势。该研究最终纳入中文文献1403篇,英文文献292篇。发文机构分析显示北京中医药大学和中国药科大学分别为中、英文文献发文量最多的研究机构;发文期刊分析显示《河北中医》《Journal of Asian Natural Products Research(亚洲天然产物研究杂志)》是麦冬研究发文量最多的期刊;关键词分析显示中文文献侧重于用药规律及临床观察研究,英文文献侧重于成分测定及药理研究,其中数据挖掘和基于细胞凋亡的药理机制或仍为将来一段时间的研究方向。展开更多
生物网络是系统生物学研究的重要内容。本文介绍了多种常用复杂生物网络可视化系统,针对Cytoscape系统在可视化的建模过程以及在建模过程中使用到的布局算法进行对比研究,并利用Cytoscape系统中丰富的插件对复杂网络数据进行分析,包括...生物网络是系统生物学研究的重要内容。本文介绍了多种常用复杂生物网络可视化系统,针对Cytoscape系统在可视化的建模过程以及在建模过程中使用到的布局算法进行对比研究,并利用Cytoscape系统中丰富的插件对复杂网络数据进行分析,包括对数据进行网络分析和更改、使用BINGO插件进行基因注释、使用AGILENT LITERATURE SEARCH(ALS)插件搜索基因相互作用文献等。展开更多
目的通过对瓜蒌薤白半夏汤相关文献进行可视化分析,了解瓜蒌薤白半夏汤研究发展状况及研究热点。方法计算机检索中国知识资源总库(CNKI)、中文科技期刊数据库(VIP)、中国学术期刊数据库(万方数据)、PubMed、Web of Science建库至2021年1...目的通过对瓜蒌薤白半夏汤相关文献进行可视化分析,了解瓜蒌薤白半夏汤研究发展状况及研究热点。方法计算机检索中国知识资源总库(CNKI)、中文科技期刊数据库(VIP)、中国学术期刊数据库(万方数据)、PubMed、Web of Science建库至2021年11月30日收录的瓜蒌薤白半夏汤研究文献。按照布拉德福文献离散律方法,采用Excel2019软件分析发文量、来源期刊、文献类型、涉及疾病等,采用Cytoscape3.9.0软件构建瓜蒌薤白半夏汤-疾病-靶点网络,采用CiteSpace5.8.R1软件进行关键词共现、聚类及突现分析,并绘制可视化知识图谱。结果纳入文献986篇,载文量最多的来源期刊为《实用中医内科杂志》(37篇,3.75%),临床应用类文献占比最高(611篇,61.97%);治疗疾病以内科疾病居多,其中以冠心病最为多见(496篇,57.5%);药理实验集中于急性心肌缺血相关研究(34篇,54.8%),作用机制涉及抑制心肌细胞凋亡、调节脂质代谢、抗氧化应激及抗炎;关键词共现分析显示,“冠心病”出现频次最高(182次,中心性为0.33);关键词聚类分析形成10个聚类标签,研究主要集中在瓜蒌薤白半夏汤对胸痹、冠心病、心悸、心力衰竭的临床治疗效果方面,以及各医家临床应用瓜蒌薤白半夏汤的经验总结。结论瓜蒌薤白半夏汤在临床应用和研究主要集中于治疗冠心病,药理实验研究多集中于脂质代谢、细胞凋亡等机制研究。展开更多
由于纵观科学结构的所谓“科学之科学”（Science of Science）正转向“科学政策之科学”（Science of Policy）的新方向，为此可以认为，纵观科学结构的科学地图（science map）将移向科学结构中包含的纵览政策的政策地图（policy map...由于纵观科学结构的所谓“科学之科学”（Science of Science）正转向“科学政策之科学”（Science of Policy）的新方向，为此可以认为，纵观科学结构的科学地图（science map）将移向科学结构中包含的纵览政策的政策地图（policy map）方向。在此背景下，基于科学根据（evidence）的政策制定可以确保其透明性。文章通过应用日本科学技术振兴机构（简称JST）构建的专利和论文整合检索系统（PATLISYS—J），介绍世界科学结构的可视化，以及将任意研究者详细分析等进行可视化的方法。展开更多
Objective Pharmacological methods were used to screen targets and signaling pathways of Ma Xing Shi Gan Decoction(MXSGD)during influenza treatments,and mechanisms underlying antiinfluenza effects were elucidated.Metho...Objective Pharmacological methods were used to screen targets and signaling pathways of Ma Xing Shi Gan Decoction(MXSGD)during influenza treatments,and mechanisms underlying antiinfluenza effects were elucidated.Methods The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)and relevant literature were searched under predefined conditions to identify the main compounds and their targets.Interactions between the target proteins were predicted using the STRING database.Gene Ontology(GO)functional enrichment analyses and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were performed on the core targets involved in the influenza protein-protein interaction(PPI)network,using WebGestalt and the reactome database.iGEMDOCK was used for molecular docking of receptors and ligands to produce docking scores,and the results were visualized using Autodock and PyMOL.Results In total,126 major compounds and their respective targets were screened.355 influenza target proteins and 1221 influenza protein interactions were predicted using the STRING database.Influenza-related signaling pathways were strongly enriched in pharmacodynamic targets of MXSGD such as cytokine signaling in immune system and signaling by interleukin.The main biological process was response to the stimulates.Molecular docking results showed that RELALicochalcone A docking elicited by MXSGD,was superior to that of other target proteins and active compounds,suggesting that the docking site is also the main effector site of MXSGD during influenza treatments.Conclusions The results showed that MXSGD exerts antiinfluenza effects by interfering with virus adsorption,inhibiting virus proliferation,influencing immune functions and protecting host cells,which may prevent inflammation-induced tissue damage.展开更多
The peripheral nervous system has the potential to regenerate after nerve injury owing to the intrinsic regrowth ability of neurons and the permissive microenvironment.The regenerative process involves numerous gene e...The peripheral nervous system has the potential to regenerate after nerve injury owing to the intrinsic regrowth ability of neurons and the permissive microenvironment.The regenerative process involves numerous gene expression changes,in which transcription factors play a critical role.Previously,we profiled dysregulated genes in dorsal root ganglion neurons at different time points（0,3 and 9 hours,and 1,4 and 7 days） after sciatic nerve injury in rats by RNA sequencing.In the present study,we investigated differentially expressed transcription factors following nerve injury,and we identified enriched molecular and cellular functions of these transcription factors by Ingenuity Pathway Analysis.This analysis revealed the dynamic changes in the expression of transcription factors involved in cell death at different time points following sciatic nerve injury.In addition,we constructed regulatory networks of the differentially expressed transcription factors in cell death and identified some key transcription factors（such as STAT1,JUN,MYC and IRF7）.We confirmed the changes in expression of some key transcription factors（STAT1 and IRF7） by quantitative reverse transcription-polymerase chain reaction.Collectively,our analyses provide a global overview of transcription factor changes in dorsal root ganglia after sciatic nerve injury and offer insight into the regulatory transcription factor networks involved in cell death.展开更多
Curcumin, the medically active component from Curcuma Tonga (Turmeric), is widely used to treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict its mechanisms of molecular action....Curcumin, the medically active component from Curcuma Tonga (Turmeric), is widely used to treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict its mechanisms of molecular action. Targets of curcumin were obtained based on ChEMBL and STITCH databases. Protein protein interactions (PPIs) were extracted from the String database. The PIN of curcumin was constructed by Cytoscape and the function modules identified by gene ontology (GO) enrichment analysis based on molecular complex detection (MCODE). A PIN of curcumin with 482 nodes and 1688 interactions was constructed, which has scale-free, small world and modular properties. Based on analysis of these function modules, the mechanism of curcumin is proposed. Two modules were found to be intimately associated with inflammation. With function modules analysis, the anti-inflammatory effects of curcumin were related to SMAD, ERG and mediation by the TLR family. TLR9 may be a potential target of curcumin to treat inflammation. (C) 2015 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.展开更多
The characterization of the interacting behaviors of complex biological systems is a pri- mary objective in protein protein network analysis and computational biology. In this paper we present FunMod, an innovative Cy...The characterization of the interacting behaviors of complex biological systems is a pri- mary objective in protein protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected pro- rein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in dis- eases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.展开更多
Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an...Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match（BNMatch） is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular networks and expresses the matching data between them by defining similar vertices and links with similar attributes. Moreover, in order to maintain consistency, their counterparts in other networks change when the nodes and edges in one of the compared networks are changed. It becomes easy for users to analyze similar networks by invoking comparison algorithms and visualizing the matching data between the networks using BNMatch.展开更多
将EFICA(Efficient Variant of Algorithm FastICA)方法与基因网络相结合分析一组阿尔茨海默病(AD)微阵列数据.根据分类结果提取特征基因集并探寻与早期AD相关的基因网络,实验结果表明,EFICA方法比传统的Fastica方法能够获得更好的分类...将EFICA(Efficient Variant of Algorithm FastICA)方法与基因网络相结合分析一组阿尔茨海默病(AD)微阵列数据.根据分类结果提取特征基因集并探寻与早期AD相关的基因网络,实验结果表明,EFICA方法比传统的Fastica方法能够获得更好的分类效果.并且通过对基因网络的研究,扩展了EFICA在生物信息学中的应用,为AD疾病的进一步研究提供新思路.展开更多
Cytoscape is one of the most popular platforms for biomolecular networks research. However Cytoscape cannot display biomolecular names according to their accession identifiers in different databases. A plugin named Ai...Cytoscape is one of the most popular platforms for biomolecular networks research. However Cytoscape cannot display biomolecular names according to their accession identifiers in different databases. A plugin named Ai2NU is designed and implemented in this paper. It can make biomolecular names displayed automatically in biomolecular networks graphs in Cytoscape by constructing a local dictionary. It is convenient for researchers to recognize biomolecules and enhance the research efficiency.展开更多
文摘麦冬是重要的滋阴药,有养阴生津、清心除烦的功效,并具有多种化学成分和药理作用,在临床应用十分广泛。科学知识图谱是可以定量、客观地展示学科研究的发展前沿和方向的有效工具。该研究搜集Web of Science(WoS)及中国知网(CNKI)与麦冬相关的中医药研究文献,采用科学计量学软件CiteSpace对文献中涉及的研究机构、期刊和关键词进行可视化分析,构建麦冬相关研究的共现网络,利用Cytoscape 3.8.2绘制麦冬-疾病-靶点网络图谱。并针对中、英文文献研究热点进行内容分析,讨论当前研究热点,总结麦冬研究中存在的不足,探讨其发展趋势。该研究最终纳入中文文献1403篇,英文文献292篇。发文机构分析显示北京中医药大学和中国药科大学分别为中、英文文献发文量最多的研究机构;发文期刊分析显示《河北中医》《Journal of Asian Natural Products Research(亚洲天然产物研究杂志)》是麦冬研究发文量最多的期刊;关键词分析显示中文文献侧重于用药规律及临床观察研究,英文文献侧重于成分测定及药理研究,其中数据挖掘和基于细胞凋亡的药理机制或仍为将来一段时间的研究方向。
文摘生物网络是系统生物学研究的重要内容。本文介绍了多种常用复杂生物网络可视化系统,针对Cytoscape系统在可视化的建模过程以及在建模过程中使用到的布局算法进行对比研究,并利用Cytoscape系统中丰富的插件对复杂网络数据进行分析,包括对数据进行网络分析和更改、使用BINGO插件进行基因注释、使用AGILENT LITERATURE SEARCH(ALS)插件搜索基因相互作用文献等。
文摘目的通过对瓜蒌薤白半夏汤相关文献进行可视化分析,了解瓜蒌薤白半夏汤研究发展状况及研究热点。方法计算机检索中国知识资源总库(CNKI)、中文科技期刊数据库(VIP)、中国学术期刊数据库(万方数据)、PubMed、Web of Science建库至2021年11月30日收录的瓜蒌薤白半夏汤研究文献。按照布拉德福文献离散律方法,采用Excel2019软件分析发文量、来源期刊、文献类型、涉及疾病等,采用Cytoscape3.9.0软件构建瓜蒌薤白半夏汤-疾病-靶点网络,采用CiteSpace5.8.R1软件进行关键词共现、聚类及突现分析,并绘制可视化知识图谱。结果纳入文献986篇,载文量最多的来源期刊为《实用中医内科杂志》(37篇,3.75%),临床应用类文献占比最高(611篇,61.97%);治疗疾病以内科疾病居多,其中以冠心病最为多见(496篇,57.5%);药理实验集中于急性心肌缺血相关研究(34篇,54.8%),作用机制涉及抑制心肌细胞凋亡、调节脂质代谢、抗氧化应激及抗炎;关键词共现分析显示,“冠心病”出现频次最高(182次,中心性为0.33);关键词聚类分析形成10个聚类标签,研究主要集中在瓜蒌薤白半夏汤对胸痹、冠心病、心悸、心力衰竭的临床治疗效果方面,以及各医家临床应用瓜蒌薤白半夏汤的经验总结。结论瓜蒌薤白半夏汤在临床应用和研究主要集中于治疗冠心病,药理实验研究多集中于脂质代谢、细胞凋亡等机制研究。
文摘由于纵观科学结构的所谓“科学之科学”（Science of Science）正转向“科学政策之科学”（Science of Policy）的新方向，为此可以认为，纵观科学结构的科学地图（science map）将移向科学结构中包含的纵览政策的政策地图（policy map）方向。在此背景下，基于科学根据（evidence）的政策制定可以确保其透明性。文章通过应用日本科学技术振兴机构（简称JST）构建的专利和论文整合检索系统（PATLISYS—J），介绍世界科学结构的可视化，以及将任意研究者详细分析等进行可视化的方法。
基金We thank for the funding support from the National Natural Science Foundation of China(No.81973670)the Natural Science Foundation of Hunan Province(No.2018JJ2297)+1 种基金the Key Program of Scientific Research Fund of Hunan Provincial Education Department(No.19A370)the Project of Research Learning and Innovative Experiment for College Students in Hunan(No.2016284,No.2016281,No.2017281and No.2018420).
文摘Objective Pharmacological methods were used to screen targets and signaling pathways of Ma Xing Shi Gan Decoction(MXSGD)during influenza treatments,and mechanisms underlying antiinfluenza effects were elucidated.Methods The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)and relevant literature were searched under predefined conditions to identify the main compounds and their targets.Interactions between the target proteins were predicted using the STRING database.Gene Ontology(GO)functional enrichment analyses and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were performed on the core targets involved in the influenza protein-protein interaction(PPI)network,using WebGestalt and the reactome database.iGEMDOCK was used for molecular docking of receptors and ligands to produce docking scores,and the results were visualized using Autodock and PyMOL.Results In total,126 major compounds and their respective targets were screened.355 influenza target proteins and 1221 influenza protein interactions were predicted using the STRING database.Influenza-related signaling pathways were strongly enriched in pharmacodynamic targets of MXSGD such as cytokine signaling in immune system and signaling by interleukin.The main biological process was response to the stimulates.Molecular docking results showed that RELALicochalcone A docking elicited by MXSGD,was superior to that of other target proteins and active compounds,suggesting that the docking site is also the main effector site of MXSGD during influenza treatments.Conclusions The results showed that MXSGD exerts antiinfluenza effects by interfering with virus adsorption,inhibiting virus proliferation,influencing immune functions and protecting host cells,which may prevent inflammation-induced tissue damage.
基金supported by the National Natural Science Foundation of China,No.31500823the Natural Science Foundation of Jiangsu Province of China,No.BK20150403the Natural Science Fund for Colleges and Universities in Jiangsu Province of China,No.16KJB180024
文摘The peripheral nervous system has the potential to regenerate after nerve injury owing to the intrinsic regrowth ability of neurons and the permissive microenvironment.The regenerative process involves numerous gene expression changes,in which transcription factors play a critical role.Previously,we profiled dysregulated genes in dorsal root ganglion neurons at different time points（0,3 and 9 hours,and 1,4 and 7 days） after sciatic nerve injury in rats by RNA sequencing.In the present study,we investigated differentially expressed transcription factors following nerve injury,and we identified enriched molecular and cellular functions of these transcription factors by Ingenuity Pathway Analysis.This analysis revealed the dynamic changes in the expression of transcription factors involved in cell death at different time points following sciatic nerve injury.In addition,we constructed regulatory networks of the differentially expressed transcription factors in cell death and identified some key transcription factors（such as STAT1,JUN,MYC and IRF7）.We confirmed the changes in expression of some key transcription factors（STAT1 and IRF7） by quantitative reverse transcription-polymerase chain reaction.Collectively,our analyses provide a global overview of transcription factor changes in dorsal root ganglia after sciatic nerve injury and offer insight into the regulatory transcription factor networks involved in cell death.
基金supported by grants from the National Natural Science Foundation of China(Grant No.81403103)Chinese Medicine Resources(Sichuan Province)Youth Science and Technology Innovation Team(Grant No.2015TD0028)+1 种基金Sichuan Province Science and Technology Support Plan(Grant No.2014SZ0156)Sichuan Province Education Department Project(Grant No.2013SZB0781)
文摘Curcumin, the medically active component from Curcuma Tonga (Turmeric), is widely used to treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict its mechanisms of molecular action. Targets of curcumin were obtained based on ChEMBL and STITCH databases. Protein protein interactions (PPIs) were extracted from the String database. The PIN of curcumin was constructed by Cytoscape and the function modules identified by gene ontology (GO) enrichment analysis based on molecular complex detection (MCODE). A PIN of curcumin with 482 nodes and 1688 interactions was constructed, which has scale-free, small world and modular properties. Based on analysis of these function modules, the mechanism of curcumin is proposed. Two modules were found to be intimately associated with inflammation. With function modules analysis, the anti-inflammatory effects of curcumin were related to SMAD, ERG and mediation by the TLR family. TLR9 may be a potential target of curcumin to treat inflammation. (C) 2015 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.
文摘The characterization of the interacting behaviors of complex biological systems is a pri- mary objective in protein protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected pro- rein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in dis- eases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.
基金supported by Key Project of Science and Technology Commission of Shanghai Municipality (No.11510500300)Ph.D.Programs Fund of Ministry of Education of China (No.20113108120022)
文摘Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match（BNMatch） is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular networks and expresses the matching data between them by defining similar vertices and links with similar attributes. Moreover, in order to maintain consistency, their counterparts in other networks change when the nodes and edges in one of the compared networks are changed. It becomes easy for users to analyze similar networks by invoking comparison algorithms and visualizing the matching data between the networks using BNMatch.
文摘将EFICA(Efficient Variant of Algorithm FastICA)方法与基因网络相结合分析一组阿尔茨海默病(AD)微阵列数据.根据分类结果提取特征基因集并探寻与早期AD相关的基因网络,实验结果表明,EFICA方法比传统的Fastica方法能够获得更好的分类效果.并且通过对基因网络的研究,扩展了EFICA在生物信息学中的应用,为AD疾病的进一步研究提供新思路.
基金Project supported by the Shanghai Leading Academic Discipline Project(Grnat No.J50103)the Ph D Programs Foundation of Ministry of Education of China(Grant No.20080280007)+1 种基金the Innovation Program of Municipal Education Commission of Shanghai Municipality(Grant No.11Y203)the Innovation Foundation of Shanghai University
文摘Cytoscape is one of the most popular platforms for biomolecular networks research. However Cytoscape cannot display biomolecular names according to their accession identifiers in different databases. A plugin named Ai2NU is designed and implemented in this paper. It can make biomolecular names displayed automatically in biomolecular networks graphs in Cytoscape by constructing a local dictionary. It is convenient for researchers to recognize biomolecules and enhance the research efficiency.
