2.网络分析2.网络分析.ppt

;内容提纲：;Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.;Microarray Data Sample ;Cytoscape---- 开源的系统生物学网络分析软件 ;Cytoscape;Cytoscape目前必威体育精装版版本: 2.7.0;Cytoscape;2;Cytoscape可以直接导入网络数据（Remote），也可以打开本地文件（Local） 。;PFN1 pp WIRE PFN1 pp XPO6 PFN1 pp APBB1IP PFN1 pp ENAH PFN1 pp MLLT4 PFN1 pp VASP PFN1 pp WASL PFN1 pp GPHN A1BG pp CRISP3 SEMG1 pp SEMG2 SEMG1 pp TGM1 SEMG1 pp PRKCA KLK3 pp PZP KLK3 pp FN1 KLK3 pp SERPINA5 KLK3 pp IGFBP3 ……. pp ……….;在导入完毕的时候出现的时候，出现如下提示框，表明有216个目标基因，203个互相联系。点击Close，结束提示框。　;一个红点表示一个生物网络节点，点击任一红点后，可在下方Data Panel窗口看到其ID信息。;导入表达数据库;点击Select;表达数据库的文件格式：;点击Open VizMapper ;;Cytoscape???plugins;BiNGO: determine which Gene Ontology (GO) categories are statistically over-represented in a set of genes. Cerebral: Given an interaction network and subcellular localization annotation, Cerebral automatically generates a view of the network in the style of traditional pathway diagrams, providing an intuitive interface for the exploration of a biological pathway or system. Cytoprophet: It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. Agilent Literature Search: build networks by extracting interactions from scientific literature.;/plugins.php;;http://www.psb.ugent.be/cbd/papers/BiNGO/;插件安装后：;GO (Gene Ontology) ;新建文件名字;Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.;取名“Gal”;Cerebral 插件;下载Cerebral 插件;http://www.pathogenomics.ca/cerebral/index.html 需要下载两个文件： cerebral2.0.jar和prefuse.jar;安装Cerebral 插件;导入数据;Import〉Node Attributes 分别导入tlr4_localization.noa和tlr4_function.noa文件 ;noa文件;点击Create Cerebral view;;Cytoprophet: 预测蛋白及结构域相互作用插件/index.php/download;从插件菜单（Plugins）中打开cytoprophet插件;首先导入cytoprophet.sif文件;;运行后，分别得到蛋白相互作用关系的窗口和蛋白结构域相互作用关系的窗口;在数据面板（Data panel）中选择要显示的节点属性;查看节点属性;;查看边的属性;Agilent Literature Search文献检索插件 /cyto_web/plugins/index.php;检索结果显示区域;如何建立beta-catenin, p53, wnt5, ifnb, nfatc, il6六个基因在皮肤黑色素瘤（Melanoma）的发生