Background： Module detection is widely used to analyze and visualize biological networks. A number of methods and tools have been developed to achieve it. Meanwhile, bipartite module detection is also very useful for...Background： Module detection is widely used to analyze and visualize biological networks. A number of methods and tools have been developed to achieve it. Meanwhile, bipartite module detection is also very useful for mining and analyzing bipartite biological networks and a few methods have been developed for it. However, there is few user- friendly toolkit for this task. Methods： To this end, we develop an online web toolkit BMTK, which implements seven existing methods. Results： BMTK provides a uniform operation platform and visualization function, standardizes input and output format, and improves algorithmic structure to enhance computing speed. We also apply this toolkit onto a drug-target bipartite network to demonstrate its effectiveness. Conclusions： BMTK will be a powerful tool for detecting bipartite modules in diverse bipartite biological networks. Availability： The web application is freely accessible at http：//www.zhanglabtools.net/BMTK.展开更多
With the popularization of microarray experi-ments in biomedical laboratories,how to make context-specific knowledge discovery from expression data becomes a hot topic.While the static“reference networks”for key mod...With the popularization of microarray experi-ments in biomedical laboratories,how to make context-specific knowledge discovery from expression data becomes a hot topic.While the static“reference networks”for key model organisms are nearly at hand,the endeavors to recover context-specific network modules are still at the beginning.Currently,this is achieved through filtering existing edges of the ensemble reference network or constructing gene networks ab initio.In this paper,we briefly review recent progress in the field and point out some research directions awaiting improved work,includ-ing expression-data-guided revision of reference networks.展开更多
Investigation of the potential therapeutic mechanisms of drug candidates is an essential step in the process of new drug discovery.With the rapid development of systems biology,recent network analyses of proteins,drug...Investigation of the potential therapeutic mechanisms of drug candidates is an essential step in the process of new drug discovery.With the rapid development of systems biology,recent network analyses of proteins,drugs,and diseases have enabled great progress in delineating the molecule mechanisms of drug candidates.However,most analyses perform a direct association between gene/protein and disease levels without considering the intermediate biological pathways regulated by the drugs.Given that a protein performs its biological roles through pathways,we propose using a novel pathway-pathway network analysis to investigate the potential therapeutic functions of the drug candidates.Many studies have demonstrated that salvianolic acid B(SalB) of Salvia miltiorrhiza is an effective therapy for cardiovascular diseases(CVD).Using molecular docking methods to identify direct interacting targets of Sal B,we collected all Sal B-regulated proteins with supporting experimental evidence in PubMed abstracts.FDA-approved CVD drugs and their corresponding targets were also collected.From a traditional drug-protein network analysis,we found that Sal B could affect ACE and REN of the renin-angiotensin-aldosterone system to relax vessels and alleviate hypertension.Subsequent pathway-pathway network analysis was attempted to study the mechanisms of Sal B in treating CVD,and demonstrated that Sal B regulates immunity/inflammation,apoptosis,ion transport and basic metabolism processes in the treatment of CVD.Regulating the immune/inflammation process may be the major mechanism of Sal B.We believe that pathwaypathway network analysis is a novel method for studying the therapeutic mechanisms of herbal ingredients.展开更多
基金This work has been supported by the National Natural Science Foundation of China （Nos. 61621003, 61422309, 61379092 and 11661141019）, the Strategic Priority Research Program of the Chinese Academy of Sciences （CAS） （XDB13040600） and CAS Frontier Science Research Key Project for Top Young Scientist （QYZDB-SSW-SYS008）.
文摘Background： Module detection is widely used to analyze and visualize biological networks. A number of methods and tools have been developed to achieve it. Meanwhile, bipartite module detection is also very useful for mining and analyzing bipartite biological networks and a few methods have been developed for it. However, there is few user- friendly toolkit for this task. Methods： To this end, we develop an online web toolkit BMTK, which implements seven existing methods. Results： BMTK provides a uniform operation platform and visualization function, standardizes input and output format, and improves algorithmic structure to enhance computing speed. We also apply this toolkit onto a drug-target bipartite network to demonstrate its effectiveness. Conclusions： BMTK will be a powerful tool for detecting bipartite modules in diverse bipartite biological networks. Availability： The web application is freely accessible at http：//www.zhanglabtools.net/BMTK.
基金This work was supported by a grant from Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences(No.2008KIP207)the National Natural Science Foundation of China(Grant No.30770497)the National Key Technologies R&D Program(No.2007AA02Z331).
文摘With the popularization of microarray experi-ments in biomedical laboratories,how to make context-specific knowledge discovery from expression data becomes a hot topic.While the static“reference networks”for key model organisms are nearly at hand,the endeavors to recover context-specific network modules are still at the beginning.Currently,this is achieved through filtering existing edges of the ensemble reference network or constructing gene networks ab initio.In this paper,we briefly review recent progress in the field and point out some research directions awaiting improved work,includ-ing expression-data-guided revision of reference networks.
基金supported by the National Natural Science Foundation of China (30900832)the Open Project Program Foundation of Key Laboratory of Liver and Kidney Diseases (Shanghai University of Traditional Chinese Medicine)+2 种基金the Program for New Century Excellent Talents in University (NCET-08-0399)the "Shu Guang" Project by Shanghai Municipal Education Commission and Shanghai Education Development Foundation (07SG22)the National Science and Technology Major Project of China (2012ZX10005001)
文摘Investigation of the potential therapeutic mechanisms of drug candidates is an essential step in the process of new drug discovery.With the rapid development of systems biology,recent network analyses of proteins,drugs,and diseases have enabled great progress in delineating the molecule mechanisms of drug candidates.However,most analyses perform a direct association between gene/protein and disease levels without considering the intermediate biological pathways regulated by the drugs.Given that a protein performs its biological roles through pathways,we propose using a novel pathway-pathway network analysis to investigate the potential therapeutic functions of the drug candidates.Many studies have demonstrated that salvianolic acid B(SalB) of Salvia miltiorrhiza is an effective therapy for cardiovascular diseases(CVD).Using molecular docking methods to identify direct interacting targets of Sal B,we collected all Sal B-regulated proteins with supporting experimental evidence in PubMed abstracts.FDA-approved CVD drugs and their corresponding targets were also collected.From a traditional drug-protein network analysis,we found that Sal B could affect ACE and REN of the renin-angiotensin-aldosterone system to relax vessels and alleviate hypertension.Subsequent pathway-pathway network analysis was attempted to study the mechanisms of Sal B in treating CVD,and demonstrated that Sal B regulates immunity/inflammation,apoptosis,ion transport and basic metabolism processes in the treatment of CVD.Regulating the immune/inflammation process may be the major mechanism of Sal B.We believe that pathwaypathway network analysis is a novel method for studying the therapeutic mechanisms of herbal ingredients.
