KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库作为整合了基因、酶、化合物及代谢网络信息的综合性数据库,在生物信息学研究中提供了非常重要的平台。首先,人工获得实验数据并将其组织为计算格式,构建成一个系统功能知识体系:包...KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库作为整合了基因、酶、化合物及代谢网络信息的综合性数据库,在生物信息学研究中提供了非常重要的平台。首先,人工获得实验数据并将其组织为计算格式,构建成一个系统功能知识体系:包括KEGG通路图,BRITE等级分类以及KEGG modules。其次,建立并完善跨物种注释步骤KO,把基因组同分子网络联系起来。文章主要介绍KEGG数据库的最新进展以及KEGG在生物信息学中的应用。KEGG特有的图形代谢通路以及KO注释,对于重构代谢网络以及跨物种的代谢网络分析提供了很好的信息,KEGG数据库在生物合成以及药物设计方面将会得到越来越广泛的应用。展开更多
Exploring the structural topology of genome-based large-scale metabolic network is essential for in- vestigating possible relations between structure and functionality.Visualization would be helpful for obtaining imme...Exploring the structural topology of genome-based large-scale metabolic network is essential for in- vestigating possible relations between structure and functionality.Visualization would be helpful for obtaining immediate information about structural organization.In this work,metabolic networks of 75 organisms were investigated from a topological point of view.A spread bow-tie model was proposed to give a clear visualization of the bow-tie structure for metabolic networks.The revealed topological pattern helps to design more efficient algorithm specifically for metabolic networks.This coarse- grained graph also visualizes the vulnerable connections in the network,and thus could have important implication for disease studies and drug target identifications.In addition,analysis on the reciprocal links and main cores in the GSC part of bow-tie also reveals that the bow-tie structure of metabolic networks has its own intrinsic and significant features which are significantly different from those of random networks.展开更多
随着功能基因组时代的到来,转录组测序技术快速发展且应用相对广泛。玉米基因组测序的完成,有力地推动着玉米转录组结构的注释和功能的深入解析。简述玉米基因组研究概况以及GS FLX、Solexa GA IIx、SOLiD等测序技术的发展,回顾转录组...随着功能基因组时代的到来,转录组测序技术快速发展且应用相对广泛。玉米基因组测序的完成,有力地推动着玉米转录组结构的注释和功能的深入解析。简述玉米基因组研究概况以及GS FLX、Solexa GA IIx、SOLiD等测序技术的发展,回顾转录组测序技术在玉米新基因挖掘、分子标记开发、代谢网络、分子进化、miRNAs等相关研究领域上的应用,为玉米复杂农艺性状的分子机制、不同发育阶段基因表达调控网络乃至分子设计育种等工作的深入研究提供参考。展开更多
One of the main tasks of post-genomic informatics is to systematically investigate all mole- cules and their interactions within a living cell so as to understand how these molecules and the interactions between them ...One of the main tasks of post-genomic informatics is to systematically investigate all mole- cules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing prin- ciples that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.展开更多
Soybean[Glycine max（L.） Merr.]is one of the world＇s major crops,and soybean seeds are a rich and important resource for proteins and oils.While ＂omics＂ studies,such as genomics,transcriptomics,and proteomics,have...Soybean[Glycine max（L.） Merr.]is one of the world＇s major crops,and soybean seeds are a rich and important resource for proteins and oils.While ＂omics＂ studies,such as genomics,transcriptomics,and proteomics,have been widely applied in soybean molecular research,fewer metabolomic studies have been conducted for largescale detection of low molecular weight metabolites,especially in soybean seeds.In this study,we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry.One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed.Among the 169 detected metabolites,104 were found to be significantly variable in their levels across tested cultivars.Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified,and metabolitemetabolite correlation analysis revealed some significant associations within the same or among different metabolite groups.Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.展开更多
文摘KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库作为整合了基因、酶、化合物及代谢网络信息的综合性数据库,在生物信息学研究中提供了非常重要的平台。首先,人工获得实验数据并将其组织为计算格式,构建成一个系统功能知识体系:包括KEGG通路图,BRITE等级分类以及KEGG modules。其次,建立并完善跨物种注释步骤KO,把基因组同分子网络联系起来。文章主要介绍KEGG数据库的最新进展以及KEGG在生物信息学中的应用。KEGG特有的图形代谢通路以及KO注释,对于重构代谢网络以及跨物种的代谢网络分析提供了很好的信息,KEGG数据库在生物合成以及药物设计方面将会得到越来越广泛的应用。
基金Supported in part by the Ministry of Science and Technology of China(Grant Nos.2003CB715900 and 2004CB720103)National Natural Science Foundation of China(Grant Nos.30500107 and 30670953)Science and Technology Commission of Shanghai Municipality(Grant Nos.04DZ19850 and 04DZ14005)
文摘Exploring the structural topology of genome-based large-scale metabolic network is essential for in- vestigating possible relations between structure and functionality.Visualization would be helpful for obtaining immediate information about structural organization.In this work,metabolic networks of 75 organisms were investigated from a topological point of view.A spread bow-tie model was proposed to give a clear visualization of the bow-tie structure for metabolic networks.The revealed topological pattern helps to design more efficient algorithm specifically for metabolic networks.This coarse- grained graph also visualizes the vulnerable connections in the network,and thus could have important implication for disease studies and drug target identifications.In addition,analysis on the reciprocal links and main cores in the GSC part of bow-tie also reveals that the bow-tie structure of metabolic networks has its own intrinsic and significant features which are significantly different from those of random networks.
文摘随着功能基因组时代的到来,转录组测序技术快速发展且应用相对广泛。玉米基因组测序的完成,有力地推动着玉米转录组结构的注释和功能的深入解析。简述玉米基因组研究概况以及GS FLX、Solexa GA IIx、SOLiD等测序技术的发展,回顾转录组测序技术在玉米新基因挖掘、分子标记开发、代谢网络、分子进化、miRNAs等相关研究领域上的应用,为玉米复杂农艺性状的分子机制、不同发育阶段基因表达调控网络乃至分子设计育种等工作的深入研究提供参考。
基金supported by the National Science and Technology Key Programs of China(Grant No.2004BA711A21)the State Key Program of Basic Research of China(Grant No.2004CB720103)+1 种基金the National Natural Science Foundation of China(Grant No.30500107)the Key Program of Basic Research of Shanghai(Grant Nos.04QMX1450,04DZ19850&04DZ14005).
文摘One of the main tasks of post-genomic informatics is to systematically investigate all mole- cules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing prin- ciples that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.
基金supported by the China National Transgenic Plant Special Fund(2011ZX08012-002 and 2013ZX08012-002)Innovative Research Team Fund(Ministry of Education,China)111 Project Fund(B14016)
文摘Soybean[Glycine max（L.） Merr.]is one of the world＇s major crops,and soybean seeds are a rich and important resource for proteins and oils.While ＂omics＂ studies,such as genomics,transcriptomics,and proteomics,have been widely applied in soybean molecular research,fewer metabolomic studies have been conducted for largescale detection of low molecular weight metabolites,especially in soybean seeds.In this study,we investigated the seed metabolomes of 29 common soybean cultivars through combined gas chromatography-mass spectrometry and ultra-performance liquid chromatography-tandem mass spectrometry.One hundred sixty-nine named metabolites were identified and subsequently used to construct a metabolic network of mature soybean seed.Among the 169 detected metabolites,104 were found to be significantly variable in their levels across tested cultivars.Metabolite markers that could be used to distinguish genetically related soybean cultivars were also identified,and metabolitemetabolite correlation analysis revealed some significant associations within the same or among different metabolite groups.Findings from this work may potentially provide the basis for further studies on both soybean seed metabolism and metabolic engineering to improve soybean seed quality and yield.
