GeneGo Map Editor 2.1
Contents
1. 5 Font FontColor BorderColor ArcHeight BackgroundColor BorderWidth ArcWidth Object type Name Tooltip Figure 8 Adding a label Adding Interactions To add an interaction first select the link tool in the toolbar the cursor will change to a dark black arrow Figure 9 Then click on an object this object will be the source object Then click on a second object for the target it can be the same object as the source After clicking the target a window will appear to create the interaction If an 12 interaction between the two objects is already present in the MetaCore database it will be listed in the DB Links tab Select the interaction and click Ok to place it on the map Figure 10 Alternatively you can click the Custom link tab to create your own interaction The custom tab contains options for specifying the interaction s effect and mechanism Possible effects include unspecified activation inhibition and No effect Possible mechanisms include unspecified any covalent modification phosphorylation dephosphorylation binding competition transformation cleavage transcription regulation class relation influence on expression complex subunit catalysis transport transport catalysis and No mechanism If No mechanism or No effect is specified the interaction hexagon will not appear on2. cursor to add interactions between objects by clicking on them E When this button is clicked use the cursor to zoom in to a specific place on the map a When this button is clicked use the cursor to zoom out from a certain place on the map Opening a New Map Click the New Map button to open a new map New maps initially contain the cytoplasm nucleus and membrane localizations Additional objects interactions and localizations can be added to the map using the Add Objects panel amp Map Editor v2 0 1 Lee File Layers View Windows Help Res l Oele A mee Me m fea i eela ool Blom S ssl BA ea Untited EJ ua Add objects me ex Network objects Proteins Compound objects R lt f gt Name or function pE Object ID Name Description No object selected Figure 4 Opening a new map Adding Objects Tools to add objects to the map can be accessed from the Add Objects panel Figure 5 The Add Objects panel is open by default when Map Editor is started To open the panel after it has been closed select Add Objects from the Windows menu The panel contains options to search for objects in the MetaCore database network objects chemical compounds proteins and reactions The Add Objects tool can also be used to add links to other maps in MetaCore custom objects localizations and labels Use the arrow buttons in the upper right corner to
3. like experiments uploaded to MetaCore Double click on the name to view the map When active data contains genes from the map the custom map will appear in the list generated from the View gt Maps option and data thermometers will appear on the custom map Data manager Microsoft Internet Explorer DES File Edit View Favorites Tools Help ar OQ gt x Poser ferao O 2 mw Address http strials genego com cgi data_manager cai Go i Links amp A GeneGo SYSTEMS BIOLOGY FOR DRUG DIS em Homepage Questions amp fi Data manager Maps MapEditor MetabL SS Data managg Data manager File Edit View Tools Help Ga i E 7 ey A x amp Activate My Data MAPS A Name y Date ee MAPS 09 18 2006 08 38 24 ee Active Data ad AKT signaling custom 09 20 2006 07 20 43 B p53 custom map v 09 18 2006 08 44 39 Custom Man 09 28 2006 02 47 18 En Properties Alt Enter Ba Copy Ctrl C cut Ctri x LA Create folder F7 X Delete F8 Rename Shift F6 Internet Figure 23 Published maps in MetaCore 26
4. radiomimetic agents ataxia telangiectasia mutated serine proggin kinase ATM is activated C Cell death 1 If the DNA damage is by UV light or UV mimetic agents ia telangiectasia and C1 Growth and differentiation Rad3 related protein kinase ATR and DNA activated protei se DNA PK are CI Immune response activated 2 ATM ATR andDNA PK belong to phosphoinositi 3 kinases family These C Proteolisis stimulated kinases signal the presence of DNA damage in cells by 1 Regulation of transcription phosphorylating proteins that initiate cell cycle arrest apoptosis DNA repair 3 4 Ef Function groups There are three basic pathways which participate in DNA damages Syduced cell response CJ Regulation of metabolism Ee Cf Disease maps ME The reaction that initiates the checkpoint arrests is phosphorylation of We cell cycle Figure 18 Opening a GeneGo map 21 Searching a Map You can use the Search objects on map panel to search the open map for objects by name or ID Enter a name or ID in the box at the top and click Search If you enter an ID number select ID in the drop down menu to the left of the search box The results will be listed in the lower window Click on a result and the object will be circled in blue on the map Map Editor v2 0 1 File Layers View J fafo v PropertiesView lej let f gi untied EER v Add objects v Search objects on map Efu s
5. shared confidentially within a customer s user group accessing their internal MetaCore server Accessing the Map Editor Java 1 4 2 except Java 1 4 2 06 and 1 4 2 07 is required on the client computer If Java is not present it is automatically installed on the client computer when Map Editor is first accessed Users can access the Map Editor by following the link on the MetaCore homepage Figure 1 After clicking on the link the Map Editor client side software will be automatically installed After the software is finished installing the Map Editor will open and ask for a database connection E MetaCore web access gate Microsoft Internet Explorer File Edit View Favorites Tools Help Q sack T x x a A PO Search Se Favorites B te a Le D B d 33 Address http itrials genego com DRE GeneGo SYSTEMS BIOLOGY FOR DRUG DISCOVERY Wem lomepage M Questions amp Answers Personal profile Logout S Data manager Maps MapEditor Metabolic networks Signaling networks Search SS Welcome to MeN Core Customer support Ein 888 592 3124 26 E mail customersupport e MetaCore sections e Information 3 Links gt 6 z A YQ MetaCore sections Data manipulation e Data manager Upload your experimental data compare multiple experiments select data for visualization Data visualization e Maps View our curated pathways e Metabolic networks View metaboli
6. the interaction arrow You can also enter a mouse over tooltip if desired The interaction can be made non directional no arrowhead by un checking the make directed interaction box When finished creating the link click the Add button to add it to the map Figure 10 To change the effect or mechanism of an interaction from the MetaCore database first click the Custom box in the interaction s properties Then the effect and mechanism drop down menus will become active Figure 12 Interaction properties As with Objects clicking on an interaction hexagon will bring up its properties on the left Figure 12 The properties include Effect The interaction s effect can be changed in this drop down menu Errors Warnings If details of the interaction effect mechanism to and from nodes differ from an interaction in the database between the same nodes an error or warning will be listed here ID Displays the ID number for the interaction if it is present in the MetaCore database Custom interactions have an ID of none Mechanism The interaction s mechanism can be changed in this drop down menu Tooltip The mouse over tooltip text displayed in MetaCore can be entered here URL The URL of the page that is opened when the user clicks on the interaction hexagon after the map has been published to MetaCore Click the go button to open the URL from the Map Editor Directed Un checking or checki
7. GeneGo Map Editor 2 1 User Manual MapEditor version 210 Copyright 2000 2007 GeneGo Inc 30 Table of Contents LAS D OIC OUD csc see secea asc aaterasameseen sees ieenayostahatad A castanoted ned 3 Accessing the Map Editor ea arananliedenn ee ee 3 Connectine tothe Databases an ei ee ee 4 NAVIGATION mn dam nine ads 5 BUOM OVE V OW siete heap E A eee aes he Hi ete A 6 Openme a New Maps ins sd aed 7 Adding ODICCES Eine nent 8 OD CT TOP IIS RSR RE Mit ne AS in ascend Guise Ste din acted ten 9 CFEGHNS A CUS om OD OCI nanas ai needed Dion 10 CrO GDS de te Rd A 11 Label Proper ES ARE A aN 11 Addie Interactions sec sud dar dou T E E 12 Thera cl On PUOP CVU ES aT AERE E NE NE E A E E 13 TPAC ON VISUAIIZATIONS o Ea N A ONR 15 Adding Localizations 17 Locali all on Proper eS RER nn ne Te enr ON Te en Din Ode 17 Savino a MAD nn A tn A tr 18 Opening a Saved Map siennes 18 Pubhishmne a MAD en ob ie 19 Opening a Saved NetWork osais une mins nine 20 Editing an Existing MetaCore Map 21 Searchin a Map nd RS Dr dendetete Dee aaa nie redondance eres 22 Oer CDOS gars en ae ao on neo hein 23 Ad US UN MOD LA A RS de dic nacht Sasa NRA Re NE ARS Sen 23 MAD PV OP CIVICS TES Rod nn tr on Gee 24 DISDIOP warmin esanda Error S sessanta ee iara EOE E EE een tenait 25 Published Mapsin Me taCOre tan ce ae ees 26 Introduction MapEditor is a Java module which enables custom editing
8. The map will be saved as an XML file You can also save the map as an image file First select Save image from the File menu Then choose a resolution in the window that appears and click Ok Then browse for a location give the image a name and click Save The image is saved as a PNG file Opening a Saved Map To open a saved to your computer in XML format first click the Open map button es or select Open map from the File menu Then browse for the file and click Open The map will be opened in a new tab amp File Layers View Windows Help ales v DIE QE als CE x code alesis eeaeee ooo Blom S eles ele Ala MA Add objects x Network objects Proteins compound objects IR DES gt Name or function marn2 Object MDM2 Ubiquitin protein ligase E3 M MTBP Mdm 2 transformed 3T3 cell MDM4 Mdm4 protein Name Description ls BE Look In J MapEditor maps creb_network xml Bi CREBsignalingNetworkMap xml Ri genegoMap703 xml C test13 xml C test14 xmi FileName ltesti3xml Files of Type XML stored maps X open cancer No object selected Figure 15 Opening a saved map 18 Publishing a Map Publishing a map makes that map available for viewing and mapping experimental data to within MetaCore To publish the active map in the editor fir
9. c networks e Signaling networks View signaling networks draw networks from your list of genes Data search a Cezrrh Figure 1 Accessing the Map Editor Connecting to the Database m Internet In order to use the Map Editor you first need to connect to the MetaCore database When the editor is first opened the connection dialog box is opened as well Select the server to connect to in the Connection drop down menu and enter your account name and password Then click the Connect button Figure 2 amp Connection dialog Eg Figure 2 Server connection dialog box Navigation The Map Editor tool is comprised of multiple windows and panels The Add Objects and Properties windows are open by default These windows can be docked into the main Map Editor window by holding Ctrl and clicking and dragging on the window header This will create a section colored in blue where the window will be docked release the mouse button to dock the window A docked window can be un docked by clicking the arrow button in the upper right corner of the window Figure 3 Opened maps are initially docked into a number of tabs The tabs can be un docked in a similar fashion The Add Objects panel contains a number of tabs for searching for specific objects adding localizations and adding labels Click the arrow buttons in the upper right corner of the Add Objects panel to scroll through these tabs A nu
10. croll to the nearest match as you type Select the desired network and click Ok Figure 17 The network will open in a new tab in the editor Objects interactions and localizations can be added and removed as with any other map in the editor amp ap Editor v0 8b IX Fie Layers View Windows Help SRA l EDER Al Ble EX 7 CEE x Zopa dd objects q x Network objects Proteins Compound objects Re al Name or function mdm2 Object ID 5 Search Name Description MDM2 Ubiquitin protein ligase E3 M MTBP Mdm2 transformed 3T3 cell _MDM4 Mdm4 protein 14 06 2006 09 20 14 06 2006 09 12 14 06 2006 02 10 _ 12 06 2006 15 12 _ 12 06 2006 08 10 _ NW ERO1Lalpha_analyze_deferoxamine2 115 NVY ERO1Lalpha_analyze_deferoxamine_ntwk 16 NT ERO1Lalpha_analyze_deferoxamine NVY c Raf 1 c Fos SHP 2 c Jun POGF R beta_network 118 NT_ c Raf 1 c Fos SHP 2 c Jun PDGF R beta 119 NW BMP receptor2_network 120INT BMP receptor2_netshot 121INW IGF 1 receptor ID2 PAX2 FGFR2 PAI1123 122 NW IGF 1 receptor ID2 PAX2 FGFR2 PAM123 U TMa 123INT _lIGF 1 receptor 102 PAG FGFR2 PA nn 124 NW BMP2_had_data 23 05 2006 TSU 125 NV from anlayze 21 05 2006 10 37 126 NW List with 65 networks no maps 20 05 2006 11 05 127 NW List with 65 networks no maps 20 05 2006 11 05 128 NW List with 65 networks
11. d drag the desired label to the map Then click on the label You can edit the label s properties to enter the label text specify the font type and size enter a tooltip and change the font border and background color The border s shape can also be changed by changing the values in the ArcHeight ArcWidth and BorderWidth fields Figure 8 Labels can be moved and linked to like any other object on the map Label properties Labels have some additional properties Font You can change the font type and size for the label text by using the drop down menus Font Color Choose a color by clicking the button to the right of the current color Then select a color from the swatches 11 BorderColor The background color can be specified in the same manor as the font color BackgroundColor The background color can be specified in the same manor as the font color ArcHeight and ArcWidth Enter numbers here to change the shape of the label BorderWidth Enter a number here to specify the thickness in pixels of the label border After editing a text property press Enter on your keyboard to keep the changes amp Map Editor v2 0 1 DEK Cra mee E ee Bere wigiwe Bes Bala MEE RIRA Acid objects 2 Localizations Custom objects _ Select label type USSA Normal process Labels af gt gt Pathological process Ex Arial v 12 Arial Plain 12
12. description Click Ok to apply any changes made Figure 21 ap Editor v0 le n Del Eola e ed afaa eaea pol EE se a e Mdm2 transformed 3T3 cell PMS Md protein z Figure 21 Map properties 24 Display warnings and errors Objects and interactions that have errors or warnings can be marked on the map by checking the Show errors and Show warnings checkboxes in the View menu Errors are circled in red and warnings are circled in yellow The error or warning description is displayed in the interaction or object properties section Figure 22 gt Map Editor v0 8b File Layers Windows Help a ea ES a HAPETE SNESE f Add objects Network objects Proteins Compound objects Re atr Name or function mim Object ID Search 7 Description j MDM2 Ubiquitin protein ligase E3 M iam DNA j MTBP Mdm2 transformed 3T3 cell MDM4 Mdm4 protein lt HTML Myc proto oncogene proteins HTML Tooltip Icon false Localization Nucleus Complex Errorsiwamings Figure 22 A warning for an incorrect localization placement 25 Published Maps in MetaCore After publishing a map from the Map Editor the map becomes available in your account on MetaCore The map will appear in the MAPS folder in the Data Manager Published maps can be shared renamed and deleted from the Data Manager just
13. e polyline This option is similar to polyline it allows you to create multiple right angles in the interaction arrow Double click the interaction and then left click on it to create another right angle The arrow can be adjusted by clicking and dragging on the red squares Right click on a red square to remove it and that angle Bezier This option allows you to create an interaction arrow in the shape of an S curve After double clicking on the interaction two red squares will appear By clicking on and dragging these squares you can form the arrow into an S curve Figure 13 amp Map Editor v2 0 1 aax Fie Layers View Windows Help Cm DERE Oe wee GORE er 5 Mec CEE RIESIA A Add objects 5 Network objects Proteins Compound obje gt Name or function ecfr Object iD Name Description R Epidermal growth factor r endothelial gro endothelial gro endothelial gro No object selected 16 Adding Localizations Localization images can also be added to the map These localizations can be used to represent how genes in one part of the cell can affect genes in another part of the cell for example Possible localizations include Golgi EPR Lisosome Membrane Mitochondria Nucleus Peroxisome Cytoplasm and Extracellular To add a localization image select the Localizations tab in the Add Objects window and then click a
14. fe aa Hal Add objects i x 3 Network objects Proteins Compound obje gt Name or function bmp Object io Name Description BMP receptor2 Bone morphogenetic pr BMP3 Bone morphogenetic pr EMP9 Growth differentiation fa BMP4 Bone morphogenetic pr BMP2 Bone morphogenetic pr BMP6 Bone morphogenetic pr BMP Bone morphogenetic pr BMP5 Bone morphogenetic pr BMP1 Bone morphogenetic pr Custom DNA dotheli netic pr netic pr BMPR1A Bone morphogenetic pr 5 Search objects on map i Ex Name 7 nf kb _ Exact match F KB Show search results Figure 19 Searching the map for NF KB 22 Other Options Adjusting map size The size of the map can be adjusted by clicking the Page setup button LE and entering a new Height and Width in the box that appears After expanding the map size click the Expand buttons to spread the objects apart so that they fit better in the expanded map space Figure 20 p Editor v0 he DEE BOR 6 e o a e d SSS Favre wees 6 SA mama MTBP Mdm2 transformed 373 cell MDM4 Mdm4 protein Figure 20 Adjusting the map size 23 Map properties The properties for the map can be accessed by clicking the Map properties button In the window that appears you can give the map a name and a
15. mber of button groups are also available at the top of the Map Editor These groups can be undocked from the main window by clicking and dragging on the left bar of the group A button group can be re docked by dragging it back to the top or by clicking the close button Many of the buttons functions are also available in the menus at the top of the Map Editor amp Map Editor v0 8b BAX File Layers View Windows Help aho DER A BO EH e a a e a ea wes 66 ANR EU ex LL D E x ID 482 Custom Add objects B x 2 Name mom Network objects Proteins Compound objects Reactions le alr j URL Name or function imdrn2 _ Exact match sss Ubiquitin protein ligase E3 Mdm2 Object ID Tooltip Search Search results Name Description MDM2 Ubiquitin protein ligase E3 Mdm2 MTBP Mdm2 transformed 3T3 cell doubl MDM4 Mdm4 protein 5 Icon lt enzyme v 5 Complex _ false Localization Cytoplasm Erorsiwamings 1 objects on map Ee RE PR RE V Show search results Search Clear search results DELLE ELA AA AEA AAA AAA AA AAA AA AAA ALAA AAA AA AAA AAA AAA AERA AAA AA AAA A AAA AA AAA A AAA AAA ADA AAA AEA AAA AAA AAA AAA A AAA AA AEAAAAAAEAA AE AAA AAA ARE AAA EEA AA AEA AREA CEE PR ERP EEE Figure 3 The M Button
16. nd drag the desired localization onto the map Figure 14 Localizations can be resized by first clicking on them Eight black squares will appear around the localization image Click and drag on one of these squares to resize the localization Figure 14 amp Map Editor v2 0 1 Jets Rho DB A As AE owe ACCRO DCE Le ne Custom objects JLabeis 4 7 Select localization type m Cytoplasm EPR Extracellular j BE x ajb a Golgi Lisosome Microsome egpowsome mitochondria mitochondria_2 j p ildren v true Lock _ false MoveWithChilren T false z Name ler Figure 14 Adding the EPR localization Localization properties Localizations also have various properties DrawChildren Unchecking this box will make any objects in the localization disappear 17 Lock If this box is checked any objects in the localization will be locked in You will not be able to move them outside of the localization image MoveWithChildren When this box is checked and the localization image is moved any objects in the localization will move as well Saving a Map A map can be saved in two formats To save a map so that you can work on it later first click the Save map button Eh or select the Save map option from the File menu then in the window that pops up browse for the folder in which to place the file and click Save
17. ng this box will remove or add an arrowhead to the interaction 13 Visualization This drop down menu contains the different arrow shape options see below Map Editor v2 0 1 ME File Layers View Windows Help Rho Olla A eee msg 0 Je 7 Sas eao ool SaS else Ra ai eE x stale Ads jects fe x Nei rork objects Proteins Compound obje De Name or function ect Object ip Search Ee Name on EGFR Epidermal growth factor r __VEGFR 3 Vascular endothelial gro _VEGFR 2 Vascular endothelial gro VEGFR 1 Vascular endothelial gro No object selected Figure 9 Creating an interaction ae C hoose interactions Fa HE Croate interaction DE interactions W make directed interaction Figure 10 An interaction that is already present Figure 11 Creating a custom interaction in the database 14 amp Map Editor v2 0 1 Jeg File Layers View Windows Help Eu CORDES wee 101 GSES Bese wees we en Tite x HE dd objec Ex Network objects Proteins compound obje gt Name or function egfr Object io Ex 7913 tom i Mechanism transcription regul v iL Effect HB activation v URL cgiiregulation link_info cgi i go Tooltip Directed v t
18. no maps 20 05 2006 11 05 TA ictuith BA No active map Figure 17 Opening a saved network 20 Editing an Existing MetaCore Map Existing maps in MetaCore created by GeneGo can be opened and edited in the Map Editor To do so first click the Map browser button dh or select Map browser from the File menu In the window that appears select the map from the various folders present on the left You can also enter a search query to search the maps by name The browser will automatically jump to the closest match as you type Then click the Load button Figure 18 The preview window will close and the selected map will open in a new tab in the editor Objects interactions and localizations may be added or removed as with any other map in the editor Map browser Search dn Next Map na DNA damages induced respMa Creation date 2005 10 05 11 a A ey al D Propionate metabolis Pyruvate metabolism C Lipid metabolism C Metabolism of mediators CJ Nucleotide metabolism ATP metabolism C ATPATP metabolism C CTPIUTP metabolism GTP metabolism C GTP XTP metabolism C IMP biosynthesis J vitamin and cofactor metabolis C Acetyl CoA links D Glutamate links Giycine links DNA damages induced response C Cell signaling C Cell adhesion CJ Cell cycle control b DNA damages induced responses If the DNA damage is double stran G The metaphase checkpoint
19. of canonical pathway maps available in MetaCore conversion of networks into map visualizations and drawing regulatory and metabolic maps from scratch A user may choose the objects for his her maps from the MetaCore content of genes proteins compounds and interactions or introduce new objects Custom maps can then be securely published added to MetaCore s standard map collection on the customer s server used as a template for mapping experimental data and or saved and shared with colleagues In fact a user can focus and organize his her wet lab or dry lab research around a set of interactive maps created in MapEditor and linked to MetaCore The custom set of maps can then be published and available in the comprehensive context of modern human biology presented in MetaCore as a set of 500 canonical signaling and metabolic maps The user is then able to work with a vast body of high throughput data for instance disease specific microarrays expression experiments available internally or in public domain databases on his her maps The data can be parsed in MetaCore placed on custom and standard maps the maps can be aligned according to relevance to imported data the gene content from multiple maps exported or explored further Such capability of meta analysis could substantially expand the focus of research of any biologist or medicinal chemist regardless of access to proprietary high throughput data The custom maps can be
20. overview Below 1s a brief description of the Map Editor toolbar buttons hd Use this drop down menu to zoom in or out to the selected percentage Click the magnifying glass button to fit the map in the window E Click this button to open a new map Click this button to save the active map to an XML file on your desktop E Click the button to close the active map Al Click this button to publish the active map for use in MetaCore ne iranl HHL y Click this button to open a previously saved map XML file EI Click this button to open the Map Browser which allows you to open a GeneGo map in the editor Click this button to open a saved network in the Map Editor ES Click this button to open the Search objects on map panel a Click this button to edit the map s name and description E Click this button to edit the map s dimensions L a j e Use these buttons to undo or redo actions respectively EEE Use these layer buttons to move the selected objects or localizations forward or backward ABE GES too amp do S These are alignment buttons Use these buttons to align the selected objects along a given line EE Use these buttons to spread the objects on the map out or move the objects closer together Le When this button is clicked use the cursor to select move or edit objects and their properties I When this button is clicked use the
21. rue Visualization Errorswarnings Figure 12 Viewing interaction properties Interaction visualizations There are six visualization options for interaction arrows Figure 12 Using these options you can shape the arrows to fit your map In all cases double click on the interaction hexagon to bring up the red adjustment squares After double clicking you can also click and drag the hexagon to move it to another location on the arrow The different interaction visualizations are Default This is simply a straight arrow Double clicking the interaction will only allow you to move the hexagon Round Selecting this option will create a curved arrow After double clicking on the interaction a red box will appear in the center Click and drag this box to set the amount of curvature desired Polyline This option will allow you to create multi angled arrows After double clicking on the interaction left click on any location along the arrow A red square will appear Click and drag the square to create the desired angle You can place and drag multiple squares to create multiple angles in the arrow Right click on a red square to remove it and its angle 15 Right angle line This option will create an interaction with one right angle After double clicking on the interaction a red square will appear at the right angle Click and drag the square to place the angle in the desired location Right angl
22. s between the newly added object and any other objects on the map Select the interactions you wish to add and click OK You can click and drag the object to move it After clicking on an object the object s properties will appear in the Properties window Figure 6 Alternatively you can double click on a search result to have the object automatically placed in its associated localization if the localization is present on the map If the object is dragged and dropped to a location outside its associated localization the localization will be placed below the object Object properties The properties for objects include Localization If localization organelles are present in this drop down menu one can be selected so that the editor will report a warning if the object is placed outside that localization on a map Complex Checking this box will place a white star on the object signifying that it is a complex of multiple genes proteins molecules Errors Warnings A message will appear here in red if there is an error or in yellow if there is a warning Icon Click this button to open a window containing all the available map icons Click on an icon in the window to change it 1f desired Name This is the name of the object as it appears on the map After changing the field press enter for the change to appear on the map ID This is the object s database ID number Tooltip The text that appears when you mou
23. scroll through the available tabs To add a database object first search for it To search by ID number check the box next to ID and enter the number in the box to the right After entering the query click the Search button The Results will then appear Click and hold on a result Then drag it over to the map window to place the object Figure 5 Sra File Layers z windows Help Re D Die 6 06 wee amp Choose links ein ow Slams Ses BR LE Add objects Network objects Proteins TCompound objects Ra di z Name or function p53 Object ID Name Description p53 Cellular tumor antigen p53 lt p53BP1 Tumor suppressor p53 bin A P53CSVTP53 regulated inhibitor of 7 P53AIP1 p53 regulated apoptosis in 4 P53DINP1a Tumor protein p53 inducibl A TP53TG5 TP53 target gene 5 protein TP53AP1 TP53 activated protein 1 i USP53 Inactive ubiquitin carboxyl t PARC p53 associated parkin like ASPP1 Apoptosis stimulating of p5 Reprimolreprimo TP53 dependant PIG11 Tumor protein p53 inducibl PRPKITP53 regulating kinase MDM1 Mdm4 transformed 3T3 cel PREG1 p53 responsive gene 1 RRM2B Ribonucleoside diphospha SER Apoptosis stimulating of p5 v No object selected Figure 5 Adding an object The object will then appear on the map Then a window will pop up containing the interaction
24. se over the object on the map URL The address opened after clicking on the object the map needs to be published and opened in MetaCore After editing a text property press Enter on your keyboard to keep the changes Untitled Vascular endothelial gro 2 Vascular endothelial gro VEGFR 1 Vascular endothelial gro Figure 6 Object properties Creating a custom object If you cannot find the object you wish to add to the map you can create a custom object by selecting the Custom objects option in the Add Objects window Click and drag the custom object onto the map Figure 7 Then click on the object on the map and edit its properties in the Properties window You can then create interactions to and from that object just as with any other object see below l amp Map Editor v2 0 1 Lice File Layers View Windows Help Rho gt 09 8 l QE eles 02e ales B arn fool EE sles Rely ja je Cr ae x KED Add objects l A Localizations Custom objects Select object type x Labels lal gt Custom ID om i Name Custom A T URL E f Tooltip Icon a protein v Complex false Localization NAY 2 Errorsiwarnings Figure 7 Adding a custom object Creating a label You can add labels to a map as well Choose the Labels option in the Add Objects window Then click an
25. st click the Publish map button ET or select Publish map from the File menu Then choose the folder in which to place the map by default the map is placed in the Custom Maps folder Finally click Ok Figure 16 When it is finished processing the map will be available for viewing and data mapping in MetaCore amp fap Editor v2 0 1 j o X Mps CA A ee e 0 Je a eee foe Elon S EE Maaja EEx MAA Add objects Network objects Proteins Compound objects IR al amp Choose sections ei Name mdm2 Alzheimer Disease A Atherosclerosis 2 OID Custom maps Ee Traditional metabolic maps z Search Aminoacid metabolism _ Search Carbohydrates metabolism 2 Name Description Lipid metabolism MDM2 Ubiquitin protein ligase E3 M Metabolism of Mediators F Nucleotides metabolism Steroid metabolism Vitamin and Cofactor Metabolism Signaling pathway maps MTBP Mdm2 transformed 3T3 cell MDM4 Mdr protein CI Overwrite No object selected Figure 16 Publishing a map to MetaCore 19 Opening a Saved Network Networks saved in MetaCore can be changed into static maps using the Map Editor In the editor click the Open Network button IE or select Open network from the File menu In the window that opens select the network to open as a map You can simply scroll through the list or you can type a partial name in the box provided The list will automatically s
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