CYTOSCAPE 使用说明

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1、Tutorial:BasicExpressionAnalysisinCytoscape-HumanSlideshow BasicExpressionAnalysisinCytoscape(30min) Handout Basic_Expression_Analysis_in_Cytoscape-Human.pdf(11pages) TutorialCurators KristinaHanspers, AlexPico, MikeSmoot Contents [hide]·1 LoadingNetwork·2 Loadingexpressiondata·3 Visu

2、alizingExpressionDatao3.1 Setthenodecoloro3.2 Setthedefaultnodecoloro3.3 Setthenodeshapeo3.4 Setthenodeborder·4 Dataanalysisfeatureso4.1 FilterNodeso4.2 Searchforanodeo4.3 ExploringNodesCytoscape isanopensourcesoftwareplatformfor integrating, visualizing,and analyzing measurementdatai

3、nthecontextofnetworks.Thistutorialwillintroduceyouto:§Combiningdatafromtwodifferentsources:experimentaldataintheformofmicroarrrayexpressiondataandnetworkdataintheformofinteractiondata.§Visualizingnetworksusingexpressiondata.§Filteringnetworksbasedonexpressiondata.LoadingNetwork§StartC

4、ytoscapeandloadthenetwork File:HumanInteractomesubset.sif.§Applytheforce-directedlayouttoorganizethelayoutofthenodes.Selectthe"Layout->CytoscapeLayouts->Force-DirectedLayout"menu.§Thenetworkshouldnowlooksimilartothis:Loadingexpressiondata§Download File:PellegrinietalData.txt.zip expre

5、ssiondataandunzipit.§Usingyourfavoritetexteditor,openthefilePellegrini_et_al_Data.txt.Thefirstfewlinesofthefileareasfollows:GeneSymbolEntrezidProbesetCREBkdcontrolpvaluefoldchangeSignCREBbindingA2M2217757_at42.2457.450.41.5yesA2ML11445681553505_at67.95206.470.110.58A2ML11445681564307_

6、a_at160.05183.440.810.95Youshouldnotethefollowinginformationaboutthefile:1.Thefirstlineconsistsoflabels.2.Allcolumnsareseparatedbyasingletabcharacter.3.Thefirstcolumncontainsnodenames,andmustmatchthenamesofthenodesinyournetworkexactly!4.ThesecondcolumncontainsEntrezGeneIDs.5.Thethirdc

7、olumncontainsAffymetrixprobesetIDs.Thiscolumnisoptional,andthedataisnotcurrentlyusedbyCytoscape,butthiscolumnmaybeusefulforanalysisinothermicroarrayanalysistools.6.Theremainingcolumnscontainexperimentaldata;averageexpressionforexperimentalandcontrolgroups,pvalueandfoldchangeforthecomp

8、ariso