CYTOSCAPE 使用说明.docx

CYTOSCAPE 使用说明.docx

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CYTOSCAPE使用说明

Tutorial:

BasicExpressionAnalysisinCytoscape-Human

Slideshow BasicExpressionAnalysisinCytoscape（30min） 

Handout Basic_Expression_Analysis_in_Cytoscape-Human.pdf（11pages） 

TutorialCurators KristinaHanspers, AlexPico, MikeSmoot 

Contents

 [hide]

∙1 LoadingNetwork

∙2 Loadingexpressiondata

∙3 VisualizingExpressionData

o3.1 Setthenodecolor

o3.2 Setthedefaultnodecolor

o3.3 Setthenodeshape

o3.4 Setthenodeborder

∙4 Dataanalysisfeatures

o4.1 FilterNodes

o4.2 Searchforanode

o4.3 ExploringNodes

Cytoscape isanopensourcesoftwareplatformfor integrating, visualizing,and analyzing measurementdatainthecontextofnetworks.Thistutorialwillintroduceyouto:

▪Combiningdatafromtwodifferentsources:

experimentaldataintheformofmicroarrrayexpressiondataandnetworkdataintheformofinteractiondata.

▪Visualizingnetworksusingexpressiondata.

▪Filteringnetworksbasedonexpressiondata.

LoadingNetwork

▪StartCytoscapeandloadthenetwork File:

HumanInteractomesubset.sif.

▪Applytheforce-directedlayouttoorganizethelayoutofthenodes.Selectthe"Layout->CytoscapeLayouts->Force-DirectedLayout"menu.

▪Thenetworkshouldnowlooksimilartothis:

Loadingexpressiondata

▪Download File:

PellegrinietalData.txt.zip expressiondataandunzipit.

▪Usingyourfavoritetexteditor,openthefilePellegrini_et_al_Data.txt.Thefirstfewlinesofthefileareasfollows:

GeneSymbolEntrezidProbesetCREBkdcontrolpvaluefoldchangeSignCREBbinding

A2M2217757_at42.2457.450.41.5yes

A2ML11445681553505_at67.95206.470.110.58

A2ML11445681564307_a_at160.05183.440.810.95

Youshouldnotethefollowinginformationaboutthefile:

1.Thefirstlineconsistsoflabels.

2.Allcolumnsareseparatedbyasingletabcharacter.

3.Thefirstcolumncontainsnodenames,andmustmatchthenamesofthenodesinyournetworkexactly!

4.ThesecondcolumncontainsEntrezGeneIDs.

5.ThethirdcolumncontainsAffymetrixprobesetIDs.Thiscolumnisoptional,andthedataisnotcurrentlyusedbyCytoscape,butthiscolumnmaybeusefulforanalysisinothermicroarrayanalysistools.

6.Theremainingcolumnscontainexperimentaldata;averageexpressionforexperimentalandcontrolgroups,pvalueandfoldchangeforthecomparison,anddataonwhetherornotthegenebindsCREB.Seethe manuscript fordetailsonthedatageneration.

NOTE:

Theexpressiondatausedinthisexamplehasbeenpre-processedtoworkwiththeinteractionnetworkused.Thedataisacompositeofdatafilesfrom Pellegrinietal,BMCCancer,2008.

▪Underthe File menu,select Import→AttributefromTable（Text/MSExcel）.

▪Click"Node"forthetypeofattributetoimport.

▪SelectthefilePellegrini_et_al_Data.txt.

▪Clickthe"TextFileImportOptions"checkbox.

▪Makesurethe"Tab"checkboxinthe"Delimiter"sectionisselectedandthatnoothercheckboxunder"Delimiter"isselected.Thepreviewshouldindicatethatitisimportingmultiplecolumnsofdata.

▪Clickthe"Transferfirstlineasattributenames"checkboxinthe"AttributeNames"section.Thepreviewshouldnowshowbeusingthefirstrowoftheinputfileascolumnnamesandtheimportwindowshouldlookliketheimagebelow.

▪Clickthe"Import"buttontoimporttheattributedata.

Nowwewillusethe NodeAttributeBrowser tobrowsethroughtheexpressiondata,asfollows.

▪SelectanodeontheCytoscapecanvasbyclickingonit.

▪Inthe NodeAttributeBrowser,clickthe SelectAttributes button 

andselecttheattributes"foldchange"and"pvalue"byleft-clickingonthem.Right-clicktoclosethemenu.

▪Underthe NodeAttributeBrowser,youshouldseeyournodelistedwiththeirexpressionvalues,asshown.

VisualizingExpressionData

ProbablythemostcommonuseofexpressiondatainCytoscapeistosetthevisualattributesofthenodesinanetworkaccordingtoexpressiondata.Thiscreatesapowerfulvisualization,portrayingfunctionalrelationandexperimentalresponseatthesametime.Here,wewillwalkthroughthestepsfordoingthis.

Setthenodecolor

▪Double-Clickthe NodeColor rowinthe VisualMappingBrowser inthe UnusedVisualProperties Section.

▪Thisactionwillmove NodeColor tothetopofthe VisualMappingBrowser.

▪Clickthe"Pleaseselectavalue!

"cellinthe NodeColor section.

▪Thiswillproduceadrop-downmenuofavailableattributenames.Select"foldchange".

▪Clickthe"Pleaseselectamapping"cellinthe NodeColor section.

▪Thiswillproduceadrop-downmenuofavailablemappingtypes.Select"ContinuousMapping".

▪Thisactionwillproduceabasicblacktowhitecolorgradient.

▪Clickonthecolorgradienttochangethecolors.Thiswillpop-upagradienteditingdialog.

▪Dragtheleft-most,redhandlealongthetopofthegradient.DragittoanAttributeValueofapprox.-1.2

▪Dragthewhitehandletoapprox0.5.YoucantypetheAttributeValueintheHandleSettingssectiontobemoreprecise.

▪Youcanalsochangethecolorofeachhandlebydouble-clickingorusingtheNodeColorselectorbuttonintheHandleSettingssection.

▪ThisshouldproduceaRed-White-GreenColorgradientliketheimagebelow,withminandmaxextremescoloredblackandblue,respectively.

▪Click'OK'tosavethegradientadjustmentdialogandverifythatthenodesinthenetworkreflectthenewcoloringscheme.

Setthedefaultnodecolor

Notethatthedefaultnodecolorofpinkfallswithinthisspectrum.Ausefultrickistochooseacoloroutsidethisspectrumtodistinguishnodeswithnodefinedexpressionvalueandthosewithslightrepression.

▪Clickthe Defaults networkiconinthe VizMapper panel.

▪Clickthe NodeColor entryandchooseadarkgraycolor.

▪Zoomoutonthenetworkviewtoverifythatafewnodeshavebeencoloredgray.

Setthenodeshape

WeimportedbothafoldchangevalueandapvalueforthecomparisonbetweenCREBkdandcontrolcells.Wecanusethepvaluestochangetheshapeofthenodessothatmeasurementswehaveconfidenceinappearassquareswhilepotentiallybadmeasurementsappearascircles.

▪Double-Clickthe NodeShape rowinthe VisualMappingBrowser inthe UnusedVisualProperties Section.

▪Thisactionwillmove NodeShape tothetopofthe VisualMappingBrowser.

▪Clickthe"Pleaseselectavalue!

"cellinthe NodeShape section.

▪Thiswillproduceadrop-downmenuofavailableattributenames.Select"pvalue".

▪Clickthe"Pleaseselectamapping"cellinthe NodeShape section.

▪Thiswillproduceadrop-downmenuofavailablemappingtypes.Select"ContinuousMapping".

▪Thiswillcreateanemptyiconinthe"GraphicalView"rowofthe NodeShape section.Clickonthisicon.

▪Thisactionwillpop-upacontinuousshapeselectiondialog.

▪Clickthe Add button.

▪Thisactionwillsplittherangeofvalueswithasliderdownthemiddlewithanodeshapeicontoeithersideoftheslider.

▪Double-Clickontheleftnodeicon（acircle）.

▪Thiswillpop-upanodeshapeselectiondialog.

▪Choosethe Rectangle shapeandclickthe Apply button.

▪Thecontinuousshapeselectiondialogshouldnowshowbothasquareandacirclenodeshapeicon.

▪Clickontheblacktriangleandmovetheslidertotheleft,toslightlylowerthat0.05,ourthresholdforsignificance.

▪Closethecontinuousshapeselectiondialogandverifythatsomenodeshaveasquareshapeandsomenodeshaveacircularshape.

Setthenodeborder

WecanusethenodebordercolorandstyletoreflectwhetheranodehasbeenfoundtobesignificantlyboundbyCREB（ref）.Thisdataisalreadyavailableinthedatasetasanattribute.

▪Double-Clickthe NodeBorderColor rowinthe VisualMappingBrowser inthe UnusedVisualProperties Section.

▪Thisactionwillmove NodeBorderColor tothetopofthe VisualMappingBrowser.

▪Clickthe"Pleaseselectavalue!

"cellinthe NodeBorderColor section.

▪Thiswillproduceadrop-downmenuofavailableattributenames.Select"SignCREBbinding".

▪Thiswillproduceadrop-downmenuofavailablemappingtypes.Select"DiscreteMapping".

▪Thiswillcreateanewrowforthevalue"yes",whichistheonlyvalueavailableforthisattribute.Clickontheemptycelltotherightof"yes",andthenclickonthesquareiconthatappears.

▪Acolorchooserwillappear.Pickacolorthatwillstandoutagainstthecolorscheme,forexampleabrightyellow.Therelevantnodesinthenetworkwillbeoutlinedinyellow.

Next,wewanttoalsochangetheborderthickness,sincethethinyellowbordercanbehardtosee.

▪Double-Clickthe NodeLineWidth rowinthe VisualMappingBrowser inthe UnusedVisualProperties Section.

▪Thisactionwillmove NodeLineWidth tothetopofthe VisualMappingBrowser.

▪Clickthe"Pleaseselectavalue!

"cellinthe NodeLineWidth section.

▪Thiswillproduceadrop-downmenuofavailableattributenames.Select"SignCREBbinding".

▪Thiswillproduceadrop-downmenuofavailablemappingtypes.Select"DiscreteMapping".

▪Thiswillcreateanewrowforthevalue"yes",whichistheonlyvalueavailableforthisattribute.Thedefaultnodeborderwidthof1.5willbeselectedtotherightof"yes".

▪Clickintheboxspecifyingthewidthandtype5.

▪Zoomingintopartofthenetwork,itnowlookslikethis:

Dataanalysisfeatures

ThissectionpresentsafewexamplesoffeaturesinCytoscapethatcanbeusedtofurtheranalyzethenetworkandassociateddata.

First,hereissomebackgroundonyourdata.Thedataisfromanexperimentinahumanmyeloidleukemiacellline.ThecAMPResponseElementBindingProtein,CREB,wasknockeddownbyshRNAandtheexpressionprofileofknockdowncellswascomparedtot