pd map user guide 010917 -

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User Guide PD map 01 September 2017

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Page 1: PD map user guide 010917 -

User Guide

PD map

01 September 2017

Page 2: PD map user guide 010917 -

01/09/2017 PDmapuserguide 1

Contents

1. Howtostart....................................................................................................................................2

1.1. Introduction............................................................................................................................2

1.2. PathwaysandCompartmentsview........................................................................................2

1.3. Biologicaloverview.................................................................................................................3

1.4. Submaps.................................................................................................................................4

2. Howtobrowseandsearch.............................................................................................................4

2.1. Browse....................................................................................................................................4

2.2. Search:GENERIC.....................................................................................................................6

2.3. Search:Howtousedruginterface.........................................................................................7

2.4. Search:Howtousechemicalinteractioninterface................................................................9

2.5. Search:HowtousemiRNAinterface...................................................................................10

3. Howtodisplayimplementeddatasets........................................................................................11

4. HowtodisplaycustomdatasetsonthePDmap.........................................................................13

4.1. Uploadandhighlightalistofelements................................................................................13

4.2. Uploadofadatafile:Datapreparation................................................................................14

4.3. Uploadofadatafile:Dataupload........................................................................................15

5. Howtoprovidecommentsandfeedback....................................................................................16

6. HowtoextractinformationfromthePDmap.............................................................................17

6.1. Exportfunction.....................................................................................................................17

6.2. Selectmode..........................................................................................................................18

7. Help..............................................................................................................................................19

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1. Howtostart

1.1. Introduction

TheParkinson’sdisease(PD)map(http://pdmap.uni.lu)• displays disease-related molecular and biochemical pathways within a neuronal cell

system,focusedonadopaminergicneuron,adjacentcells(i.e.,astrocytes,microglia)andcellularstructures(i.e.,blood-brain-barrier,synapticterminals)

• integratesmorethan1300manuallycuratedpublicationsandover250entriesfrompublicdatabasessuchasReactomeorKEGG(asofSep,2017)

• hasanintuitive“GoogleMaps”displaythatenableseasynavigation

• iscomposedof

• species(here:elements,entities)suchasgenes,proteins,molecules,complexes,annotatedwithrelevantdatabaseentries

• reactions(orinteractions)describingrelationsbetweenspecies,annotatedwithrelevantliteratureand/ordatabaseentries

• “LEGEND”button(rightupperside,bluepanel)providesdetailsontheformatofelementsandinteractions

1.2. PathwaysandCompartmentsview

“Pathwaysandcompartments”isthedefaultviewprovidinganoverviewonthecontent.

Fig.1:Pathways(grey)andcompartments(coloured)viewofthePDmap

• provideshierarchicalinformationonthecellularstructures,processesandcomplexes

• clickinacompartmentprovidesadditionalinformationintheleftpanel

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• zooming out/in provides higher level compartment view or a more detailed view onmolecularspeciesandinteraction,respectively(seealsochapter2)

• select“Network”forapurenetworklayout

• select“Empty”foracolourlessnetworkview,usefulwithindatasetsoverlayonthePDmap(seealsochapter3and4).

1.3. Biologicaloverview

• TogetaviewofthebiologicalsystemsthataremodelledinthePDmapclickonthebutton“SHOWOVERVIEW”(Fig.2;redrectangle).

Fig.2:BiologicaloverviewofthePDmap

• Eachfigurecontainsthreestandardbuttonsintheleftuppercorner(“home”,“back”,”tomap”)tonavigatethroughthepicturesortogototherespectiveareainthePDmap

• Clickingonthemarkedareas leadsyoutomoredetailedpicturesofthesurroundedareaorifnofurtherdownstreampictureisavailableitlinkstotherespectiveareasinthePDmap.

Importantfortabletandsmartphoneuse:

Donottiptothelinks inthecaseyouhaveenlargedthebiologicalview.ThelinkstothePDmaponlyworkproperwhenthebiologicalviewhashisoriginalsize.

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1.4. Submaps

• Tomaintain overall structure of the PDmap, some parts of themain networkwheredisplayedinseparate,moredetailedsubmaps.

• The submaps are fully operational; i.e., search functions and data display workssimultaneouslyonthewholePDmapandonthesubmaps.

• Enter submaps by clicking the "SUBMAPS" tab . Click onmagnifier to enter thereceptivesubmap.

• Alternatively,youmayclickondedicatedelementsinthemapandopenitfromtheleftsideinformationpanel.

2. Howtobrowseandsearch

2.1. Browse

• Anintuitive“GoogleMaps"displayenableseasynavigationthroughthePDmap.

• ClickingonanyelementinthePDmap(e.g.,proteins,moleculesorphenotypes)providesdetailedannotationsandlinkstoexternaldatabases,whicharedisplayedintheleftpanel(Fig.3),presumablySERCHGENERICisactive.Otherwise,theinformationisvisibleonthebottomoftheleftpanel(seeFig.11:CREPPBprotein).

Fig.3:Screenshotshowingannotationsoftheprotein:MARK2(MAP/microtubuleaffinity-regulatingkinase2)

Anno

tatio

ns

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• Byclickingonthebubblepinnedtotheelement(Fig.4Aredarrow),additionalinformationisdisplayedinapopupbox.

• Forgenes,miRNAsandproteinsaspecialpopupboxenablesthesearchforinteractingdrugs,chemicalsandmiRNAs.Firstclickontheelement,thenonthecolourednumberaboveandthentherelatedcheckbox(“Showall”)(Fig.4).

• Formoreinformationonthedifferenttoolsfordrugs,chemicalsandmiRNAsinteractionseerelatedchapters2.3,2.4,and2.5.

Fig.4:AdditionalinformationandfunctionsinrelationtoMARK2displayedaspopup.

• Clickingonaconnectionlinebetweenelements(Fig.5)providesdetailedinformationonthe underlying reaction (coloured in blue), displayed in the left panel. This includesinformationonreactantsandlinkstotheunderlyingsources(i.e.,PubMed,ReactomeorKEGG).

Fig.5:Screenshotshowingannotationsofreactionre4026:MUL1mediatesubiquitinationofMFN2.Activatedreactioniscolouredinblue.

(A) (B)

Anno

tatio

ns

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2.2. Search:GENERIC

• The"GENERICSEARCH"functionislocatedintheupperpartoftheleftpanel.

• Allelements(e.g.,genes,proteins,smallmolecules,complexes)aresearchable.

• Searchfunctionalsoworkswithsynonyms.

• Searchformultipleelements:separatenamesbysemicolon(seeFig.6).

• Clickon“PERFECTMATCH”reducesthesearchtothoseelementsthatexactlycorrespondtotheinput.

• ThelocationofthesearchedspeciesisdisplayedonthePDmapbycolouredcircles.

• Resultsfromsearchesformultipleelementsaredisplayedwithdifferentcolours.

• Theleftpanelprovidesannotationsontheelementsandthereactiontypesincludinglinkstoexternaldatabases.

• Searchforreactions:typein:reaction:reXXXX(XXXX=reactionnumber).

• Searchforpublicationsandrelatedinteraction:typepubmed:XXXXXXX(whereXXXXXXX=PubMedID).

• Searchforpublicationsalsoworkswiththespecificpublicationlist.Under“INFO”youfindthe linktothe listofthecurrentpublicationscurated intothePDmap.This list is fullysearchableandcontainslinksbacktothePDmap.

• Clickingon“CLEAR”(rightuppercorner)willremoveallsearchresultsfromthePDmap

Fig.6:SearchforMitofusin2(MFN2)andMulan1(MUL1):All locationsofMFN2(redcircle)andMUL1(bluecircle)aredisplayedinthePDmap.Leftpanelshowsannotations.

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2.3. Search:Howtousedruginterface

• The“DRUG”interfaceallowstosearchforpotentialdrugtargetswithinthePDmap.

• Activatethe“DRUG”tabunder“SEARCH”.

• Typedrugnames(synonymsorbrandnamesalsowork)inthesearchfield.

• Separatemultiplesearchbysemicolon

• PotentialtargetsarefetchedfromthedrugdatabasesDrugBankandChEMBL,displayedandmarkedinthePDmapbynumberswithinacolouredrectangle.

• Additionalinformationconcerningthedrugsandthepotentialtargets,includinglinkstodrugdatabasesandPubMedisprovidedintheleftpanel.

(A)

(B)

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Fig.7:Searchforthedrug“Mirapex”.(A)InformationpaneldisplaysinformationonPramipexoleasMirapexisa brand name for the drug Pramipexole. Drug targets are displayed in the map. (B) Pramipexole targetsdopaminereceptors(DRD2andDRD1).(C)Thebubblepinnedtothetarget(e.g.,DRD1)providesinformationondruginteractionandoffersadditionalfunctionalitiestosearchforotherdrugs,chemicalormiRNAthatinteractswiththeDRD1protein(seealsoFig.4B,Fig.8,Fig.9).

Pleasenote:• Ifwithinamultiplesearchseveraldrugshitthesameelement,thebubbleswilloverlap

andonlytheonefromthesecondsearchisvisibleonthatelement(seeFig.8)

• Thesamehappenswhensearchqueriesfromdifferenttoolstargetingthesameelementin thePDmap.Only thebubble from the first search is visibleon theelement that istargetedbythetwoormoresearchqueries.

• Allresultsarealwaysdisplayedintheleftpanel.

• Allresultsaredisplayedsimultaneouslyinapopupinformationfieldwhenclickingonthebubblepinnedtothetarget(seeFig.4;Fig.7C,Fig.8andFig11).

• Attheendofthelist,theleftpanelshowsalsotargetsthatarenotinthePDmap(seeFig.9).

(C)

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2.4. Search:Howtousechemicalinteractioninterface

• The“CHEMICAL”interfaceallowstosearchforpotentialinteractionsofchemicalswiththePDmapelementsbasedontheComparativeToxicogenomicsDatabase(ctdbase.org).

• OnlyinteractionsthatareannotatedtothediseasetermParkinson’sdisease(MeSHID:D010300)intheCTDdatabaseareconsidered.

• Activate“CHEMICAL”tabunder“SEARCH”.

• Type in the full name of a chemical according to the ctdbase/chem database;abbreviationsorsynonymsdonotwork(e.g.,MTPTdoesnotworkbut1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine).

• Ifthechemicalnameincludescomma(s),placeasemicolonbehindthenametoavoidasegmentationofthenameduringprocessing.

• Alwaysseparatemultiplesearchbysemicolon.

• PotentialtargetsarefetchedfromtheComparativeToxicogenomicsDatabase,displayedandmarkedinthePDmapbyanumberwithinacolouredcircle.

• Additionalinformationconcerningthechemicalandthepotentialtargets,includinglinkstoCTDdatabasesandPubMedareprovidedintheleftpanel.

Fig.8:Searchfortheinteractiontargetsof“rotenone”and“hydrazine”.Informationpaneldisplaysinformationon “hydrazine”. Interacting species are labelled in themap (green bubbles for hydrazine; blue bubbles forrotenone).Clickingonframednumberabovethetarget(e.g.,greenframed“3”)providesinformationonthetarget (i.e.,HSPA9)andchemical interactionsandoffersadditional functionalities to search forotherdrugs,chemicalormiRNAthatinteractswiththetarget(seealsoFig.4;Fig.7C,andFig11).Pleasenote:Ifwithinamultiplesearchseveraldrugshitthesameelement,thebubbleswilloverlapandonlytheonefromthesecondsearchisvisibleonthatelement.

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2.5. Search:HowtousemiRNAinterface

• The“MiRNA"interfaceallowstosearchforpotentialtargetsofmiRNAwithinthePDmapelementsbasedonthemiRNAdatabase:miRTarBase.

• OnlytargetinteractionsthathavestrongevidenceaccordingtomiRTarBasecriteria(i.e.,reporterassays,westernblotorqPCRanalysis)areconsidered.

• Activate“MiRNA”tabunder“SEARCH”.

• Type in the miRNA ID, use only mature sequence IDs e.g., hsa-miR-125a-3p (see:www.mirbase.org).

• Separatemultiplesearchbysemicolon.

• Matchingtargets fromthemiRTarBasearedisplayed in thePDmapbypinnedbubbles(here:colouredtriangles).

• AdditionalinformationconcerningthemiRNAsandthepotentialtargets,includinglinkstomiRTarBaseandPubMedisprovidedintheleftpanel.

Fig.9:Searchfortargetsofhsa-miR-125a-3p.Leftpaneldisplaysinformationonhsa-miR-125a-3panditstargets.Targetsaremarkedbypinnedbubbles(greentriangles)inthePDmap.Clickingonthepinnedbubbleprovidesinformation on miRNA interactions and offers additional functionalities to search for other miRNA, drugs,chemicalthatinteractswiththetarget.LeftpanelshowsalsotargetsthatarenotinthePDmap(here:GPC4).

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3. Howtodisplayimplementeddatasets

• Thevisualizationofspecificdatasetsondifferentialgeneregulationisaccessibleviathe“OVERLAYS”tab(leftpanel).Differentdatasetsareindicatedunder“GENERALOVERLAYS”.

• Ageingbrain:Differentiallyexpressedgenes inhealthyagingbrain.EnricoGlaab(LCSB)contributedthisdataderivedfromAllenBrainAtlasdatabase.red:strongerexpressioninagedbrain;blue:lowerexpressioninagedbrain.See:GlaabandSchneider,2015.

• PDsubstantianigra:Differentialgeneexpression(FDR<=0.05)fromtheanalysisofeighttranscriptome data sets, comparing human post mortem brain samples from PD vs.healthycontrols.red:strongerexpressioninPD;blue:lowerexpressioninPD.See:Fujitaetal.,2013.

• PDUKGOProject genes: Genes annotatedby the Parkinson's diseaseGOAnnotationProject.darkgreen:highprioritygenelist,lightgreen:Parkinson’s-relevantprotein.See:Foulgereal.,2016.

• Theexpressiondatacouldbedownloadedunder“Data”(note:thevaluecolumninthedownloadedlistshowsnormalizedexpressionvalues)

• ClickboxestodisplaytherespectivedatasetonthePDmap.

• Pathwaysandcompartmentviewprovidesanoverviewoncellularprocessesaffectedbythevisualizeddata(Fig.10A)

• Detailed differential expression (red rectangle: up regulated, blue rectangle: downregulated)isbestvisibleusingthecolourlessoverlay“Empty”(Fig.10B).

(A)

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Fig.10:OverlayofthePDsubstantianigradatasettothePDmap.(A)Pathwaysandcompartmentview.(B)Emptyview

• Displayingmultipledatasetispossiblebytickingseveralcheckboxesinthe“View”column.Results from different data sets are simultaneously displayed by subdivided colouredrectangles(Fig.11)

• Additionalinformationisprovidedwhenclickingonthespecies(Fig.11)

Fig.11:OverlayofPDsubstantianigradatasetandageingbraindatasettothePDmap.ClickingonCREBBPprovided detailed information in a pop up box and on the bottom of the information panel. In addition,informationonInteractingdrugs,chemicalormicroRNAcanbedisplayed(seeChapters:4,5,and6)

(B)

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4. HowtodisplaycustomdatasetsonthePDmap

• Apersonalaccountisneededtouploaddata.

• Theaccountisforfree.

• Clickonthe“INFO”tab.Clickon“Requestanaccount”underUSERDATA.

• Usernameandpasswordwillbeprovidedbye-mail.

• Theaccountenablestheuploadof100separatedatasets.

• Afterlogin,userpersonaldataaredisplayedintheINFOtab.

• Touploadowndatasets,clickonthe“OVERLAYS”tab.Thisopensthemenufordatasetuploadandmanagement(“USER-PROVIDEDOVERLAYS”)

• Under“Addoverlays”youfindtwopossibilitiestouploaddatasetsandhighlightelementsonthePDmap(seeFig.12)

• Uploadandhighlightalistofelements

• Uploadalistofelementnamesandrelatedexpressionvalues(astxt.file)

Fig.12:Screenshot:“Addoverlays”form.

4.1. Uploadandhighlightalistofelements

• Clickon“Addoverlays”andfillintheform.

• Name(default)

• Description(freetext)

• Providelistofelements(oneperline)

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• ThislistmustcontainthenameofelementsasitappearsinthePDmap(e.g.,HGNCnameforproteinsandgenes;CHEBInameforsimplemolecules)

• Thelistmaycontainnamesfordifferentelementtypesatthesametime(seeFig.13A)

• ClickUPLOADstartstheprocess

• ThenewfilewillappearinUSER-PROVIDEDOVERLAYS.

• Ashortreportwillbesendbymail(“MapViewernotification”).

• DataarevisualizedbygreencolouronthePDmapafterclickingtheviewbox(Fig.13B).

Fig.13:Upload(A)alistofelementstothePDmapandvisualisation(B)

4.2. Uploadofadatafile:Datapreparation

• Datafileneedstobeuploadedasatxt.filethatconsistsoftwocolumns

• firstcolumn(headline=name)containsHGNCgenesymbols

• secondcolumn(headline=value)containsvaluesbetween-1and1

• AsbothproteinsandgenesaredefinedinthePDmapbytheuniformHGNCidentifierandHGNCgenesymbol,dataderived fromproteinorgeneexpressionwillbedisplayedongeneandproteinspeciesinthePDmap.

• Touploaddatafromotherspeciesthanhuman,thespecies-specificidentifiersneedtobetranslatedtoHGNCidentifiers.

• The differential expression values (fold changes) needs to be normalized into a rangebetween-1to1(seeFig.14).

(A)

(B)

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Fig.14:Differentialgeneexpressiondata(excelfile)wereeditedandtransformedintoatxt.filebeforeupload.Normalizationappliedhere:foldchange(f.c.)>5isset1;f.c.<-5set-1;f.c.between-1.5and1.5isset0;f.c.between-5and-1.5aswellas1.5and5arenormalizedbydividingthevalueby5.

4.3. Uploadofadatafile:Dataupload

• Clickonthe“OVERLAYS”tab.Thisopensthemenufordatasetuploadandmanagement(“USER-PROVIDEDOVERLAYS”)

• Clickon“Addoverlays”

• Fillinform

• Name(default)

• Description(freetext)

• Clickon“Browse”anselectthefiletobeuploaded

• Click“UPLOAD”tostarttheprocess

• ThenewfilewillappearinUSER-PROVIDEDOVERLAYS.

• Ashortreportwillbesendbymail(“MapViewernotification”).

• DatacouldbevisualizedonthePDmapbyclickingonview.Colorcode:BluefordownregulationandRedforupregulation

• Elementsareautomaticallycolouredbythefollowingcolourcodesinaccordancetotheirdedicatedvalues

HGNCsymbol foldchange normalization

HMOX1 14.26 1SRXN1 6.79 1GSTA2 4.97 0.994DDIT3 4.6 0.92ANXA3 4.15 0.83NFE2L2 3.55 0.71GCLM 3.39 0.678GSR 1.89 0.378SRXN1 1.81 0.362TXNRD1 1.75 0.35NQO1 1.59 0.318MFN1 1.52 0.304GSS 1.5 0.3BCL2 1.42 0NDUFA8 -1.47 0BECN1 -1.53 -0.306GSK3B -1.53 -0.306DNM1L -1.54 -0.308ATP50 -1.56 -0.312KEAP1 -1.58 -0.316CYCS -1.59 -0.318AMBRA1 -1.65 -0.33MFN2 -1.67 -0.334BCL2L1 -1.68 -0.336ATP5D -1.77 -0.354UQCRC1 -2.06 -0.412BAD -2.09 -0.418CAMK2G -2.2 -0.44DNAJC5 -2.34 -0.468CAMK2A -2.57 -0.514HSPA8 -4.57 -0.914CAMK2B -7.8 -1SLC1A1 -13.34 -1

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• Pleasenote:

• Combiningdisplayofmultipledatasetsfrom“GENERALOVERLAYS”and“USER-PROVIDEDOVERLAYS”ispossiblebyclickingdifferentdatasetsunder“View”.Resultsaredisplayedbysubdividedcolouredrectangles(seeFig.11)

• Ingeneral,allPDmapelementscanbeindividuallycolouredonthePDmap.Ifyouliketocolourelementsindividuallycontactusdirectly

• To upload data from other species (e.g., mouse), gene and protein names has to betranslatedtohumanHGNCidentifier.

• Alluploadeddataareaccessiblebythesystemadministratorsduetotechnicalreasonsbuttheyarenotvisiblebyanyotheruser.

5. Howtoprovidecommentsandfeedback

• RightclickwiththemouseinthePDmapatthepositionwherethecommentisrelatedto(note:thisfeaturedoesnotworkontabletsandsmartphones).

• Clickon:“Addcomment”, fill intheform(usethedropdownlist for“Type”)andpresssendbutton(Fig.15).

• Thecurationteamwillbenotifiedonnewcommentsandrespondtothemimmediately.

• Thecomment(withoutpersonalinformation)willbevisibleonthePDmapif“Pinned”ischecked(setbydefault)

Fig.15:Screenshotshowsthecommentfield

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• To see all pinned comments, click on the button “COMMENTS” (red circle, left uppercorner,Fig.16).

• Clickingonthecommenticon“ ”inthePDmapdisplaysthecontent(seeFig.16)

Fig. 16: Screenshot after activating the “COMMENTS” button (red circle), displaying position of all pinnedcomments.Detailsofthespecificcommentonre4026isvisibleafterclickingontherelatedicon“ ”.

6. HowtoextractinformationfromthePDmap

6.1. Exportfunction

• GotoINFOtapandclickon“EXPORT”button(redarrow)

Fig.17:Exportfunction

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• Usethetab“ELEMENTEXPORT”toselectspecificelementsfordownload.

• Usethetab“NETWORKEXPORT”toselectspecificnetworksfordownload(onlySIFfiles).

• Usethetab“GRAPHICS”todownloadwholePDmapandthesinglesubmapsasSVGfile

• Note:ThewholePDmapcouldbedownloadedunder“sourcefile”.

Fig.18:Exportfunction:ScreenshotshowsexampleforELEMENTSEXPORT.HereproteinsrelatedtoCellDeathpathwaywereextracted.HGNCsymbolandUniportidentifierwereusedforannotation.Note:onlygreencolouredannotationsarefeasible.

6.2. Selectmode

• EnablestheexportofcertainareasofPDmapareaasmodel(CellDesignerxml.file)orasimage(PNG,PDF).

• RightclickwiththemouseinthePDmapintheareayouliketoexport.

• Clickon“Selectmode”(Fig.19).

• Clickingaroundtheareaofinterestwillgenerateaframe(Fig.20).

• Assoonastheframeisclosedthecontentcanbeexported.

• Clickingrightmousebuttonwithintheframe(Fig.20).

PathwayCelldeath HGNC_SYMBOL:ADD1 UNIPROT:P35611Celldeath HGNC_SYMBOL:AKT1 UNIPROT:P31749Celldeath HGNC_SYMBOL:AKT2 UNIPROT:P31751Celldeath HGNC_SYMBOL:APAF1 UNIPROT:O14727Celldeath HGNC_SYMBOL:ATG12 UNIPROT:O94817Celldeath HGNC_SYMBOL:ATG5 UNIPROT:Q9H1Y0Celldeath HGNC_SYMBOL:BAD UNIPROT:Q92934Celldeath HGNC_SYMBOL:BAK1 UNIPROT:Q16611Celldeath HGNC_SYMBOL:BAX UNIPROT:Q07812Celldeath HGNC_SYMBOL:BBC3 UNIPROT:Q96PG8Celldeath HGNC_SYMBOL:BCL2 UNIPROT:P10415Celldeath HGNC_SYMBOL:BCL2L1 UNIPROT:Q07817Celldeath HGNC_SYMBOL:BCL2L11 UNIPROT:O43521Celldeath HGNC_SYMBOL:BID UNIPROT:P55957Celldeath HGNC_SYMBOL:BMF UNIPROT:Q96LC9Celldeath HGNC_SYMBOL:CAPN1 UNIPROT:P07384Celldeath HGNC_SYMBOL:CAPN2 UNIPROT:P17655Celldeath HGNC_SYMBOL:CASP2 UNIPROT:P42575Celldeath HGNC_SYMBOL:CASP3 UNIPROT:P42574Celldeath HGNC_SYMBOL:CASP6 UNIPROT:P55212Celldeath HGNC_SYMBOL:CASP7 UNIPROT:P55210Celldeath HGNC_SYMBOL:CASP8 UNIPROT:Q14790Celldeath HGNC_SYMBOL:CASP9 UNIPROT:P55211Celldeath HGNC_SYMBOL:CHCHD2 UNIPROT:Q9Y6H1Celldeath HGNC_SYMBOL:CRADD UNIPROT:P78560Celldeath HGNC_SYMBOL:CTNNB1 UNIPROT:P35222

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Fig.19:Generationofaframetodefineregionforexport

Fig.20:Exportoftheselectedarea(greycoloured)asSBMLfile

• Clickon“Exportasmodel”todownloadthecorrespondingxmlfile(CellDesignerSBML)orSBGN-MLfile.

• Clickon“Exportasimage”todownloadanimagefile(PNGorPDF).Pleasenote“Exportasimage”alwaysgeneratesrectangles”

7. Help

IncaseofanyproblemsorquestionsregardingthePDmapfunctionalitiespleasecontactmarek.ostaszewski@[email protected].