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
目的：通过网络药理学方法初步探讨茵陈五苓散的作用机制。方法：本研究基于中药系统药理学技术平台、蛋白数据库和String数据库,分别获取茵陈五苓散中化学成分,及其对应靶点、疾病并构建化合物-靶点,靶点-疾病网络,蛋白相互作用网络,...目的：通过网络药理学方法初步探讨茵陈五苓散的作用机制。方法：本研究基于中药系统药理学技术平台、蛋白数据库和String数据库,分别获取茵陈五苓散中化学成分,及其对应靶点、疾病并构建化合物-靶点,靶点-疾病网络,蛋白相互作用网络,通过生物学信息注释数据库（DAVID）注释数据库对靶点进行基因本体生物学过程（gene ontology biology process,GO-BP）富集分析及基因组百科全书（Kyoto Encyclopedia of Genes and Genomes,KEGG）通路分析。结果：共获得58个候选化合物,103个靶点,11个中枢（hub）靶点及262种疾病,关键靶点涉及肿瘤坏死因子（TNF）,过氧化物合成酶2（PTGS2）,ESR1等,疾病以肿瘤、免疫和内分泌为主。GO-BP条目146条,参与信号转导、转录翻译、促增殖抑凋亡、细胞组成和氧化应激条目等5种生物过程。KEGG信号通路108条,含靶点数目较多的信号通路主要涉及肿瘤、病毒、寄生虫等。结论：本研究系统地探讨了茵陈五苓散的候选成分所对应的靶点及作用机制,为今后的临床研究及进一步的开发为新药提供了思路。展开更多
Although many studies on the fishery biology of jumbo flying squid, Dosidicus gigas, have been conducted in the coastal areas within Exclusive Economic Zones （EEZs） of various countries due to its commercial and eco...Although many studies on the fishery biology of jumbo flying squid, Dosidicus gigas, have been conducted in the coastal areas within Exclusive Economic Zones （EEZs） of various countries due to its commercial and ecological importance, limited biological information is available from waters outside these EEZs. In this paper, we examined D. gigas fishery biology from waters outside Chilean, Peruvian and Costa Rican EEZs, based on the fishery data collected by Chinese jigging vessels during 2006 to 2010. The dominant mantle lengths olD. gigas were 350-450 mm, 250-400 mm and 250-350 mm outside Chilean, Peruvian and Costa Rican EEZs, respectively. Size structure analysis show that a medium-sized group existed mostly in the waters outside the Chilean and Peruvian EEZs, whereas a small-sized group occurred mainly in the waters outside the Costa Rican EEZ. The longevity of the squid outside the Costa Rican EEZ was less than 10 months, while most of those outside Chilean and Peruvian EEZs were about 1-1.5 years and very few large individuals were 1.5-2 years old. A higher percentage of mature individuals existed outside Costa Rican EEZ implying the region as a potential spawning ground, while lower proportions of mature squid outside the Peruvian and Chilean EEZs indicated that spawning may be occurring outside our study area. Spatial differences in sizes at maturity of the squid are thought to be result from different environmental factors especially different temperature and nutrition among the three areas. Stomach-content analysis showed that cannibalism was important in the diet of D. gigas. Stress generated by jigging may increase the incidence of cannibalism.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。
文摘目的：通过网络药理学方法初步探讨茵陈五苓散的作用机制。方法：本研究基于中药系统药理学技术平台、蛋白数据库和String数据库,分别获取茵陈五苓散中化学成分,及其对应靶点、疾病并构建化合物-靶点,靶点-疾病网络,蛋白相互作用网络,通过生物学信息注释数据库（DAVID）注释数据库对靶点进行基因本体生物学过程（gene ontology biology process,GO-BP）富集分析及基因组百科全书（Kyoto Encyclopedia of Genes and Genomes,KEGG）通路分析。结果：共获得58个候选化合物,103个靶点,11个中枢（hub）靶点及262种疾病,关键靶点涉及肿瘤坏死因子（TNF）,过氧化物合成酶2（PTGS2）,ESR1等,疾病以肿瘤、免疫和内分泌为主。GO-BP条目146条,参与信号转导、转录翻译、促增殖抑凋亡、细胞组成和氧化应激条目等5种生物过程。KEGG信号通路108条,含靶点数目较多的信号通路主要涉及肿瘤、病毒、寄生虫等。结论：本研究系统地探讨了茵陈五苓散的候选成分所对应的靶点及作用机制,为今后的临床研究及进一步的开发为新药提供了思路。
基金Supported by the National Natural Science Foundation of China(No.NSFC41276156)Innovation Program of Shanghai Municipal Education Commission(No.13YE091)+5 种基金Industrialization Project of National Development and Reform Commission(No.2159999)Project of Shanghai Science and Technology Commission(No.12231203900)National High Technology Research and Development Program of China(863 Program)(No.2012AA092303)Shanghai Leading Academic Discipline Project(Fisheries Discipline)National Distant-Water Fisheries Engineering Research Centerthe Scientific Observing and Experimental Station of Oceanic Fishery Resources,Ministry of Agriculture
文摘Although many studies on the fishery biology of jumbo flying squid, Dosidicus gigas, have been conducted in the coastal areas within Exclusive Economic Zones （EEZs） of various countries due to its commercial and ecological importance, limited biological information is available from waters outside these EEZs. In this paper, we examined D. gigas fishery biology from waters outside Chilean, Peruvian and Costa Rican EEZs, based on the fishery data collected by Chinese jigging vessels during 2006 to 2010. The dominant mantle lengths olD. gigas were 350-450 mm, 250-400 mm and 250-350 mm outside Chilean, Peruvian and Costa Rican EEZs, respectively. Size structure analysis show that a medium-sized group existed mostly in the waters outside the Chilean and Peruvian EEZs, whereas a small-sized group occurred mainly in the waters outside the Costa Rican EEZ. The longevity of the squid outside the Costa Rican EEZ was less than 10 months, while most of those outside Chilean and Peruvian EEZs were about 1-1.5 years and very few large individuals were 1.5-2 years old. A higher percentage of mature individuals existed outside Costa Rican EEZ implying the region as a potential spawning ground, while lower proportions of mature squid outside the Peruvian and Chilean EEZs indicated that spawning may be occurring outside our study area. Spatial differences in sizes at maturity of the squid are thought to be result from different environmental factors especially different temperature and nutrition among the three areas. Stomach-content analysis showed that cannibalism was important in the diet of D. gigas. Stress generated by jigging may increase the incidence of cannibalism.
