Pathway Visualization: User`s Manual
Contents
1. Figure 11 After folding a set of nodes a new node with name pathway xyz replaces the selected nodes 13 Pathway Viewer Metabolism of glucocorticoids and mineral corticoids SEE File Tools Layout Actions Kemia Help gt E amp A R a Hide Cofactors and Regulators Display Cofactors and Regulators Common Molecules Hide Show Overview And Inspector Hide Show Gene Window Hide Show StatuBar cAMP 5 Set Substrate Product Node Color Set Substrate Edge Color Set Product Edge Color Display Connected Pathways Connect Disconnect Processes Involving Cofactor or Enzyme Turn On OFF Regulatory Factor Editing Reset Regulatory Factor Nodes 114 154 v gt Pathway Metabolism of glucocorticoids and mineral corticoids Organism unspecified lt Figure 12 The Options main menu items Options menu allows various toggle operations and changing of the nodes edges colors The options under the Options menu are as shown in Figure 12 e Hide Unhide All Cofactors Hides unhides all cofactors e Hide Unhide All Regulatory Factors Hides unhides all activators inhibitors regulators e Common Molecules Hides or Displays common molecules on the graph To check the current common molecule list or delete a molecule from the list use the Common Molecules tab on the Overview Property Window Figure 13 a b To add a molecule to the common molecule list use the popup menu from the graph Figure 14 e Hide Show O2. Selects a set of node s edge s Multiple nodes edges can be selected by pressing the control key down and selecting the objects A rectangle area is selected by pressing the mouse and dragging over the area that needs to be selected Mouse Pan Moves the graph up down on the canvas After selecting the mouse pan the picture of a hand appears on the screen Pressing down the left button of mouse and dragging the hand upwards moves the graph upwards on the canvas and dragging the hand downwards moves the graph downwards on the canvas Marquee Zoom Marks a section area to zoom in Figure 20 and 21 Pathway Viewer Biosynthesis of Riboflavin FMN and FAD PB Fie Tools Layout Actions Options Help Figure 20 Marquee zoom to select a working area After the selection of the area is over the screen in Figure 23 appears 21 Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help SH SRROAR G Spr ABH DEAA SSS SSS SSS SSS SSS SSY SOOOEEEEEEEEEEEEEELOREREEEEEEEE Figure 21 After selecting a working area by marquee zoom tool e Interactive Zoom Zooms in out of the entire graph After the interactive zoom is selected a magnifying glass picture appears Pressing down the left button of mouse and dragging the magnifying glass upwards zooms out and dragging the magnifying glass downwards zooms into the graph Figure 22 and 23 illustrate the zoom in and zoom out e Create
3. The right portion of the pathway viewer displays the visualization graph of the selected pathway or process Add Node Edge e Nodes can be added to the main graph window by using Create Node in the tools menu or by clicking the tool bar icon e Users can set the node edge properties such as shape color by using the inspector property window Delete Graph Objects e Users can delete a set of node edge by first selecting the graph object with Select tool and pressing the delete key on the keyboard e After deleting an object all the information associated with the object is lost Therefore this function must be used with care Move or Delete a Subgraph e A subgraph is defined by selecting a rectangle area on the active window e After selecting a subgraph it can be moved or deleted as a unit Tool tips e When users move the mouse over a graph object a tool tip is shown For a pathway graph the tool tip shows the source of the pathway For a process the tool tip shows the process name 30 9 Genome Viewer Window The Genome Viewer draws the genes involved in a pathway in an organism It can hide and displayed from the Option menu At present only human and mouse genes are available Users can select species from the top dropdown list From the second dropdown list users can select a gene After a gene is selected from the list the gene is highlighted in the Genome Viewer by changing color to red In addition the pr
4. Properties Common Mols Pathway Metabolism of glucocortic Organism unspecified a Common Molecules Delete Clear b Figure 13 The Tab open the common molecules window a and delete a molecule from the list b 15 a Pathway Viewer Biosynthesis and degradation of Biotin File Tools Layout Actions Options Help SH GQ RMAQGN FH A HBHe P gt Queries Graph Manipulations gt Display all processes consuming or producing this molecu Set this molecule as Common Molecule Mi lt i gt Pathway Biosynthesis and degradation of Biotin Organism unspecified Figure 14 The pop up window that defines common molecules The user may add molecules into the common molecule list 16 3 Graph Pop Up Menu Options Based on the graph right clicked object from the main active window different popup menus are displayed 3 1 Substrate or product node pop up menu options e Queries Figure 15 o Synonyms of this molecular entity list all the synonyms of this molecules in result panel of the main form o Pathway and Process involving this molecular entity list all the processes and pathways involved in this molecules in result panel of the main form e Graph Manipulations o Display all processes consuming or producing this molecule the graph window draws all processes related to this molecule o Set this molecule as common molecule set this molecule as common mo
5. molecules on the graph 5 Main Display Window the active main display window that provides editing 6 Genome Viewer the tool to draw genes on chromosomes It can be hidden and displayed as need from MenulOptionslHide Show Gene Window 7 Status Bar the bar display pathway name and current selected organism Right click on the current selected organism will lead the popup menu to reset the organism It can be hidden and displayed as need from MenulOptions Hide Show Status Bar The overview window and the object properties window can be resized by dragging their border or hidden from the main menu by selecting Options Hide Show overview and inspector Figure 5 shows the Pathway Viewer and its above listed 7 components ey ae a E Fit 7 Fah Pathway Viewer Folate pathway Sele File Tools Layout Astions Options Help TH SRRA GN Ee BD BH 2 human X dihydrofolate r 3 N 1 a 2a 3 4 Node Prope v 5 Font Arial A l r 7 B lt He 9 Tommen Dihydrofole 10 j gt 11 E 12 4 on 4 gt Pathway Folate pathy Organism unspecified v Figure 5 The Pathway Visualization tool interface with its five components main menu bar toolbar overview property window common molecules window main display window Genome Viewer and status bar The toolbar contains in addition to the usual options such as opening a file the following toolbar buttons a Select Selects a set o
6. Node e Create Edge e Fit In Window 22 S Pathway Viewer Biosynthesis of Riboflavin FMN and FAD AAR Fie Tools Layout Actions Options Help SH SRROAR GS EH ABH P Selected Graph Properti 7 Properties Comn 4 gt Pathway Biosynthesis of Riboflavin FM Organism unspecified Figure 22 Graph zoos out S Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help SH GR RMAQ GS r N BHH PAA Anass sss SS SSS i OPPPEEEPPLET REPEL EEE EE EA Selected Graph Properti Biosynt Nadas 20 xj gt v Properties Comn 4 gt Pathway Biosynthesis of Riboflavin Organism unspecifie Figure 23 Graph zoom in The overview window displays a rectangle to indicate the currently displayed area in the main active window 23 Layout e Hierarchical layout layout the graph hierarchically e Symmetric layout layout the graph symmetrically Options e Hide Display cofactor and Regulatory factors To toggle all cofactors and regulatory factors on the graph e Hide Unhide common molecule Hide or display the common molecules on the graph Hide Display Overview Inspector window To toggle the overview and property window on the left pane 24 5 Overview Window The upper leftmost corner of the main window is the overview window It gives an overview of the graph The square appearing in this window indicates the graph portion that we are obser
7. Tab Figure 19 To delete a split molecule just select the molecule from the Split Molecules List and click Merge 19 Pathway Viewer Biosynthesis and degradation of catecholamines SEE File Tools Layout Actions Options Help SH SGQ RMAQ Gs tH ABH Search for an Entity z Search Common Maec Split Molecules gt Delete all bend points Split the substrate product node this edge connected to mo asa Merge Display Hnetonet wz lt B Properties Commo 4 gt Pathway Biosynthesis and degradai Organism unspecified Figure 18 The popup menu over an edge File Tools Layout Actions Options Help eH SR RMAQ GS 6 2 BHe M Search for an Entity Search Nometmepir Metnepiri Common Molecules M SplitMolecules 4 Merge Display clear Hnethonel Ja E Properties Common Mols Pathway Biosynthesis and de Organism unspecified Figure 19 After split the molecule SAH from the graph this molecule is added into the Split Molecules List 20 4 Tool Options The various options provided in the Main Menu can be used by pulling up the appropriate menu option or by using tools Following are the tools provided by the Pathway Viewer File Tools Open Opens a graph file Save Saves the current graph file Print Prints the current graph file Print Preview Prepares a print preview of the file Select
8. area is selected by pressing the mouse and dragging over the area that needs to be selected After Select menu item is selected the graph object properties are shown in the object properties window e Pan Moves the graph on the canvas up down left right It allows the user to manually drag the focal point of the display graph After selecting this item a picture of a hand appears on the screen Pressing down the left mouse button and dragging the hand upwards moves the graph upwards on the canvas and dragging the hand downwards moves the graph downwards on the canvas e Marquee Zoom Selects an area of the graph and zooms into it It creates a marquee that allows the user to enlarge and focus in on the view of a selected rectangular area When the user releases the left mouse button the selected area becomes the new viewing area e Interactive Zoom Zooms in out the graph After this tool is selected a magnifying glass picture appears While pressing down the left mouse button dragging the magnifying glass upwards zooms out and dragging the magnifying glass downwards zooms into the graph For Pan Marquee Zoom or Interactive Zoom tools the user needs to left click on any object on the main display window hold the left mouse button and move or drag the 10 mouse over objects The difference between Marquee Zoom and Interactive Zoom is that Marquee tool zooms into the selected area and the interactive tool zooms into the whole
9. from the Status bar 32 11 Tips for Pathway Browser 1 When double click on any where on the toolbar a context menu with the same functions as the main menu will pop up 2 Press F12 from the Pathway Browser interface to show the context menu of the Pathway Viewer 3 Inthe Pathway Browser if the there is no child nodes under the topmost pathways node double click on this node will get all available pathways 4 Double click on any pathway or process in the Pathway Browser will draw the pathway or process on the Pathway Viewer window KT03 KITAMI T Data for Folate and Homocysteine Pathways in Mouse and Human Department of Genetics CWRU Unpublished Manuscript 2003 MG98 Michal G Biochemical Pathways An Atlas of Biochemistry and Molecular Biology Wiley Spektrum 1998 ISBN 0471331309 33
10. Version 2 0 Date 7 10 2004 Report 13 Pathway Viewer Tool User Manual Center for Computational Genomics Division of Computer Science Department of Genetics EECS Department Case Western Reserve University Case Western Reserve University Cleveland OH 44106 Cleveland OH 44106 1 Pathways System Pathway Visualization Tool Living organisms behave as complex systems that are flexible and adaptive to their surroundings At the molecular level organisms consist of intricate networks of molecular reactions which are often called biochemical pathways In order to maintain visualize and ultimately analyze organism functions that result from biochemical pathways the Genome Pathways System is being developed The system contains a pathways database and the associated tools to store compare query and visualize biochemical pathways The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways The ultimate goal of the system is to describe utilize and predict systems functions and behaviors of living organisms As of July 2004 the components that the project is comprised of are as follows Pathway Browser Windows and Net Pathway Viewer including Genome Viewer Windows and Net Pathway Editor Windows and Net Pathway Explorer Windows and Net J Pathway Viewer Unix Macintosh Windows and Java To better understand the chemica
11. de Since it changes the size of the pathway graph a layout algorithm is applied after the expansion of a process Invisible Nodes Invisible nodes do not represent any molecular entities and hence are made invisible They serve the purpose of retaining the relationship between substrates the catalyzing protein and products by connecting substrate nodes to the catalyzing protein node and catalyzing protein node to product nodes Hierarchical Layout The hierarchical layout draws the molecular creation precedence relationships in a pathway graph hierarchically It emphasizes hierarchical dependencies by placing graph nodes at different levels The hierarchical style offers a wealth of features including the tailoring options constraints and edge routing Edge Routing Arc shaped edges require multiple points to be defined Edges are routed through all these points to give the edge an arc shape PRPP AMP PPI 2 3 p2 glyceerate _ 2 7 6 C Mn Mg m Tryptophan l GDP ADP ATP alpha D ribose 5 P alpha D ribo alpha D ribo Figure 4 Expanded process and collapsed process All involved molecules are drawn in the expanded view left After the process is collapsed the process is drawn as single node with the EC number Organisms and Organism Groups In the current database following the Biochemical Pathways Atlas MG98 we have three organism groups namely animals plants and yeasts and prokarya and an addit
12. ecules Figure 27 Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help eH GR RMBQ G Slp BH e e Search for an Entity Riboflavin FMN Search Common Molecules co2 CoA H20 Delete ear M Split Molecules lt gt Properties Common Mols Pathway Biosynthesis of Rib Organism unspecified Figure 27 The Common Molecules and Split Molecules Window consists of 3 components the search for an entity pane Common Molecules and Split Molecules From the search for an entity you can search the entity on the graph Choose a molecule or a process from the dropdown list and click Search the entity is highlighted on the graph with different color Figure 28 28 EE Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help SH GQ RMAQ GS FH ABH Search for an Entity Riboflavin FMN ATP Common Molecules co2 CoA H20 Delete Clear M Split Molecules Merge Display Clear lt gt Properties Common Mols Pathway Biosynthesis of Rib Organism unspecified Figure 28 Search for an entity on the graph The Common Molecules window lists current common molecules You can delete selected molecules from the list The Split Molecules Window lists current split molecules You can merge the selected molecule Please see the Main Menu section for details 29 8 Main Display Window
13. f graphic objects b Mouse Pan Moves the graph up down on the canvas c Marquee Zoom Marks a section area to zoom in d Interactive Zoom Zooms in or zooms out the entire graph e Create Nodes Adds nodes to the main display window f Create Edges Adds edges to the main display window g Hierarchical Layout Draws the graph hierarchically h Symmetric Layout Draws the graph symmetrically i Fit In Window Makes the graph fit in window j Expand View Displays hides regulatory factors and cofactors k Hide Display common molecules hides unhides all common molecules on the graph 1 Overview Property Window hides displays the overview window and property window on the left pane 2 Main Menu Options The pathway viewer provides the following pull down menus e File Tools Layout Actions Options Helps These menus provide multiple options as indicated below File menu options See Figure 6 Pathway Viewer Metabolism of glucocorticoids and mineral cortic SEE AG Tools Layout Actions Options Help RI MaQlias s e A BHle Save As Print Setup 1 falpha hydr Print Preview Print Exit 1 1 1 145 NADPH H NADPH H 1 7alpha hydr 11 deoxycort NADPH H v lt i gt Pathway Metabolism of glucocorticoids and mineral corticoids Organism unspecified Figure 6 The File main menu items e Open Opens an existing tom graph in
14. graph e Create Node Creates nodes in the current graph e Create Edge Creates edges in the current graph Pathway Viewer Metabolism of glucocorticoids and mineral corticoids DBR File BEHS Layout Actions Options Help Select QQ gw S amp ot i H Pan 17alpha hydr Marquee Zoom Interactive Zoom Create Nodes Create Edges 1 1 1 145 NADPH H NADPH H Selected Graph Properties 17alpha hydr 11 deoxycort Untitled P y n 1 NADPH H Background Cok __ blm o mssen a Fimen T A MM Figure 8 The Tools main menu items Layout menu Pathway Viewer supports only the hierarchical layout and Symmetric layout at present The hierarchical layout style shows the precedence relationships in a graph and is commonly used to represent organizational dependencies process models software call graphs workflows and information management system dependencies The hierarchical layout algorithm divides the nodes of a graph into levels It then directs edges from levels with lower level numbers topmost levels in a top down drawing to levels with higher level number bottommost levels in a top down drawing If the graph has cycles a minimal number of edges are chosen to point against the overall flow Then the nodes in each level are sorted such that the number of edge crossings is small Finally the exact node positions are determined and the edges are routed The hierarchical algorithm s constraint
15. gth Two or Less from Given Molecular Entity a pathway graph is drawn in a separate window showing the query results Figure 2 Pathway Structure Reachable in Two Steps oea lunspeciied gt Pathway Biosynthesis and degradation of ascorbat Molecular Entity 2 3 dioxo I gulonate M View the pathway graph cas _ Figure 2 Query result may be displayed as a graph This manual describes the features of the Pathway Viewer However we also briefly illustrate the features of the Pathway Browser since it is first used to select pathways for the Pathway Viewer to display Section 2 describes the main menu options Section 3 describes the pop up menu options Section 4 describes the toolbar options Section 5 discusses the overview window Section 6 explains the object properties window Section 7 depicts the common molecules split molecules window Section 8 depicts the main display window Section 9 explains the Genome Viewer Finally section 10 depicts the status bar 1 1 Definitions of commonly used terms Pathway Pathways are the sequential and cumulative actions of genetically distinct but functionally related molecules They consist of processes reactions which in turn consist of molecular entities Each process in each pathway begins with specific substrates uses various combinations of cofactors activators inhibitors and regulators and ends with products that are chemically modified substrates Molecular Entity The ge
16. ional organism group general for processes that exist in general pathways A process in a general pathway refers to a process that is common to all organism groups We grouped processes that exist in any one or more organism groups but not necessarily common to all under the organism group unspecified Finally as specific organisms we have mouse and human Pathways Database System consists of the following components see figure 1 e Main Menu Bar at the top e Pathway Browser tree View of Pathways Processes and Molecular Entities Left window e Query output window Upper right window Displays the textual output of queries Pathway Visualization window lower right window This window is managed by the Pathway Viewer as an internal window The Pathway Viewer consists of the following components 1 Main Menu Bar 2 Toolbar 3 Overview Object Properties Window the overview window provides a read only view of the entire main display graph with a movable marquee rectangle indicating the region displayed in the active window Object Properties window provides an object properties inspector which displays the properties of selected graph objects Some of the properties such as node and edge color may be edited through this window It can be hidden and displayed as need from both MenulOptions Hide Show Overview and Inspector and the toolbar 4 Common Molecules Search Window the tab for setting common molecules and searching
17. l interactions taking place in nature biologists need mechanisms to visualize pathways and processes Towards this goal a graphical interface is developed which allows formulating queries using graphical icons as well as visualizing query outputs in the form of graphs in various abstraction levels For example the user can have a pathway graph drawn showing as many details as he she chooses Or the user can have a pathway graph showing the inter connections of different pathways where some pathways may be abbreviated as nodes as opposed to sub graphs The goal of the pathway visualization is to facilitate data discovery by providing a robust collection of visualization capabilities This user manual describes the Pathway Viewer only The Pathway Browser Tool is a tool that hierarchically lists the pathways processes and molecular entities in the database and allows users to a view textual information and b launch the pathway viewer that visualizes pathway graphs The Pathway Viewer of the Pathway System provides a visual interface to biochemical pathways stored in the underlying database The Pathway Viewer is basically a graph drawing manipulation querying and storage tool Pathway Viewer provides an intuitive and highly visual means for biochemists to study query save open and curate biological pathways The tool supports ad hoc querying of the pathways data as well as menu driven queries Figure 1 shows the Pathway Browser user inte
18. lecule if it is not a common molecule Pathway Viewer Metabolism of glucocorticoids and mineral corti SEE File Tools Layout Actions Options Help eH Sa RMaQ Gs 2 BH e A Aldosterone n H a Synonyms of this molecular entity Graph Manipulations gt Pathways and Processes involving this molecular entity 1 3 99 6 Acc 11 beta 21 di s5 lt E Pathway Metabolism of glucocorticoids and mineral corticoids Organism unspecified Figure 15 The popup menu over a node Depending on the node type substrate product enzyme or process different menu items may show The figure shows the menu items after right clicking a substrate product node 17 3 2 Enzyme or process node pop up menu options Figure 16 e Queries o Synonyms of this molecular entity list all the synonyms of this molecules in result panel of the main form o List all genes involving this process list all genes in the selected organisms involved in this process in result panel of the main form Figure 17 e Graph Manipulations o Draw human genes of this process in GeneViewer draw and highlight all human genes involved in this process in the Genome Viewer window o Draw mouse genes of this process in GeneViewer draw and highlight all mouse genes involved in this process in the Genome Viewer window Pathway Viewer Folate pathway File Tools Layout Actions Options Help eH SR ROAR Gs 6 QA BMH e A Synonyms of this molecular entity Genes
19. neral name given to any entity participating in a process Catalyzing Protein The enzyme that catalyzes any reactions EC Number Enzyme Commission EC number describes the type of catalytic activity of the enzyme A single protein can have more than one catalytic function thus multiple EC numbers Substrate A molecular entity which is an input to a chemical reaction process Product A molecular entity produced as a result of a reaction process Co factor In A molecular entity that participates as a secondary input to a chemical reaction and results in a secondary output cofactor out to the reaction Co factor Out A molecular entity that is produced as a secondary output of a chemical reaction Activator A molecular entity that activates a reaction Inhibitor A molecular entity that binds to an enzyme and interferes with its activity by preventing the formation of the enzyme substrate complex or its breakdown into enzyme and product Regulator Either an activator or an inhibitor that regulates a reaction or the function of the molecule is unknown at the present time Process Any reaction involving molecular entities A process has zero i e a non enzymatic process or one catalyzing enzyme one or more substrates and products zero or more co factor ins co factor outs inhibitors or activators A sample process is drawn in Figure 3 The substrates of the process are indicated by circular nodes at the top products a
20. ocesses that this gene product involved in are highlighted on the graph by changing the process node to pink Figure 29 After users click on a gene on the Genome Viewer pane the detail information of the clicked gene is shown on the Query Result Panel of the Pathway Browser and the processes that use this gene are highlighted on the mina display window Currently only Folate and Homocysteine pathway has complete human and mouse gene data KT03 The remaining pathways data is from the Gene Atlas MG98 where instead of specific organisms organism groups e g animal plants are provided Pathway Viewer Folate pathway File Tools Layout Actions Options Help eH SR RMAQ Gr 5 101ne Pyle A 5 10me hery gt Pathway Folate pathway Organism unspecified CO etemecys kl Sinner Y Figure 29 After a gene is selected from the list the gene is highlighted in the Gene Viewer and the processes that this gene product involved in are highlighted on the graph 31 10 Status Bar The Status Bar is used to display the pathway name and current selected organism information It can be hidden and displayed from the Option menu Right click on the selected organism will lead to context menu to let you reset the organism Pathway Viewer Folate pathway File Tools Layout Actions Options Help SHER RMAQ GS EH B y unspecified Pathway Folate pathway Organism unspecified Figure 30 To reset the graph organism
21. ow horizontally by dragging and moving the splitters between the overview window and the main window and by vertically dragging and moving the splitter between the overview window and the inspector window Users can hide the overview window and the inspector window to make a bigger working area by using the menu Options Hide Show overview and inspector 26 6 Inspector Object Properties Window The window appearing below the overview window is the object property window This window indicates the properties of the selected object visual properties as well as Molecular Entity details For example if a reaction node is selected the properties shown in figure 26 are displayed Users can change the visual properties of the selected object using the object properties window Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help cH SGA RMAQ Gs 5 2 BH Arial A Ellipse E Properties Comr 4 gt Pathway Biosynthesis of Riboflavin Organism unspecified Figure 26 The inspector window and the main display window Some of the properties of the graph object may be set through the inspector window 27 7 Common Molecules and Split Molecules Window The Common Molecules and Split Molecules Window can be bringing to front by clicking the Common Mols tab on the Over Property window It consists of 3 components the search for an entity pane Common Molecules and Split Mol
22. re also indicated using circular nodes at the bottom The oval shaped nodes on the right side indicate cofactor ins and cofactor outs The red T shaped nodes on the left hand side indicate inhibitors the green horizontal lines on the left hand side indicate activators and the blue line with arrow head indicates regulators The catalyzing protein is indicated using a square shaped node at the center of the process When the mouse is pulled over to the enzyme node the enzyme name is displayed Processes can be reversible or irreversible cofactor ins gt AMP n oatectersns 2 7 6 Q enzyme 2 enzyme 7 PPI 2 3 p2 glyceerate Tryptophan GDP ADP Figure 3 A process and its associated molecular entities Common Molecules In pathways common molecules such as H2O CO2 PI O2 appear in multiple processes Connecting multiple processes due to common molecules makes the graph visually cluttered Therefore for each occurrence of a common molecule an independent node is created and drawn in the respective process Collapsed Process Collapsing a process hides all activators inhibitors regulators cofactor ins and cofactor outs Collapsing a process graph displays the remainder of the pathway graph as is Figure 4 Expanded Process Expanding a process re displays the process graph i e activators inhibitors regulators cofactor ins cofactor outs and catalyzing protein nodes associated with the process no
23. rface and how to draw a pathway or a process by the Pathway Viewer A graph can be drawn in an internal window which is at the lower right area of the Pathway Browser or drawn in a separate window Genomes Pathway Browser 2 0 metabolic pathways File view Query WebResources Customize Help Qe Pathways Synonyms of these molecular entities Type of the molecular e Biosynthesis anc entity is basic_molecuies Biosynthesis anc Find molecular entities involved in activation and inhibition List all reversible processes Tabulate the details of molecular entities involved Molecular Entities involved in each process of this pathway List all related pathways List all genes involved in this pathway View the pathway graph in an external window view the pathway graph in a specific organism g j N View the pathway graph in the internal window Set pathway organism Metabolic Pathways Signaling Pathways Pathway Biosynthesis and degradation of Bi Organism unspecified Figure 1 The Pathway Browser user interface and how to invoke Pathway Visualization Tool facility Textual results of queries are displayed in the upper right window as illustrated in Figure 1 Also separate multiple external windows can display multiple pathway graph visually For example by clicking the view the pathway graph check box in the query form of Query Pathways Paths of Len
24. system gives precise control over the final drawing and emphasizes dependencies by placing a graph s nodes at different levels The symmetric layout style produces graph layouts that emphasize the symmetries inherent in a graph s topology Cofactors and regulatory factors are hidden after symmetric layout Actions menu The options under Actions menu are as shown in Figure 9 11 Pathway Viewer Metabolism of glucocorticoids and mineral corticoids SEE File Tools Layout tmnt Options Help Hide Selected 11 af BH elg Unhide All 17alpha hydr Fold Selected Unfold Selected Unfold All Fit In Window 11 1145 4 1 gt NADPH H NADPH H 1 7alpha hydr 11 deoxycort NADPH H gt Pathway Metabolism of glucocorticoids and mineral corticoids Organism unspecified 114 154 x lt Figure 9 The Actions main menu items e Hide Selected Hides selected graph objects Hiding a node simply makes the node as well as its connected edges invisible The node and its associated edges are still in the graph but just not shown on the canvas Hidden nodes and edges can later be unhidden In a visualization of a very large graph details may make the graph difficult to understand Hiding common molecules such as H2O and CO2 makes the pathway graph compact and neat Unhide All Unhides all the nodes edges e Fold Selected Folds the selected parts of the pathway graph Folding removes a selected se
25. t of nodes from a graph and inserts them into a newly created fold graph that contains the graph objects to be folded The selected part of the graph is folded and a fold sign appears on that part of the graph Folding lets users remove and reintroduce graph objects and allows them to view the removed graph objects in a separate folder node A folder node containing the removed items can itself be folded into another folder node along with other nodes and edges Unfolding allows nested reintroduction of items that previously were folded into the folder node Figure 10 and 11 e Unfold Selected Unfolds the selected folded part of the pathway graph Unfold All Unfolds all the folders on the pathway graph Fit in Window Fits the entire graph into the current window After resizing the main display window the graph automatically fits the window 12 a Pathway Viewer Biosynthesis of Pantothenate Coenzyme A an SEE File Tools Layout Actions Options Help CH 46QRMAQ G l para a w v E z s cae Pathway Biosynthesis of Pantothenate Coenzyme A and Holo Organism unspecified Figure 10 Before folding a set of nodes a Pathway Viewer Biosynthesis of Pantothenate Coenzyme A and SEE File Tools Layout Actions Options Help SH SG6QRMAQ GS FH ABH ee Pre P W pa Oo Patwahy xyz o 5 Mg we 2 7 7 3 Mi gt lt Pathway Biosynthesis of Pantothenate Coenzyme A and Holo amp 4 Organism unspecified
26. the main display window A tom file uses the text format and contains information about the position dimensions and view object specifications for each element of the graph e Save As Saves the pathway graph displayed in the main display window as a tom file locally By default the name of the file is the pathway name process name e Print Setup Sets up various print options Users can print either the whole graph or the window on which the input focus is or selected area nodes amp edges The print setup options are as shown in Figure 7 e Print Preview Displays an image of how the output pages look like if they are printed e Exit Exits the graph drawing applications Print Entire Graph Print Current Window Print Current Selection m Scale By Multi page Printing Pages Page Columns fi V Print Page Numbers C Actual Size Paga Rowi i JV Print Crop Marks c Zoom Level Other Caption IW Print Border IV Print Caption Font Width j Color z V Print Background ea JV Print Grid Position Bottom Right x Page Setup Cancel Defaut Help Figure 7 Print setup options Tools menu The various tools provided under Tools menu are as shown in Figure 8 e Select Selects a node edge or an area containing a set of nodes and or edges of the graph Multiple nodes edges can be selected by pressing the control key down and selecting the objects A rectangle
27. verview And Inspector Hides displays the Overview Property window e Hide Show Gene Window Hides displays the Genome Viewer window e Hide Show Status Bar Hides displays the status bar on the bottom of the graph which displays the current selected organism and the pathway name e Set Substrate Product Node Color To change all substrate and product node color as preferred e Set Substrate Edge Color Changes all substrate edge colors as preferred e Set Product Edge Color Changes all product edge colors as preferred Display Connected Pathways Displays other pathways that are connected to this pathway by sharing consuming or producing a molecule e Connected Disconnected Processes Involved in Cofactor and enzyme leads to the sub menu items that connect disconnect processes that are not connected to the main graph 14 e Turn On Off Regulatory Factor Editing Turns on off the activator inhibitor regulator rectangle editing The default is turned off After turned on the system allows the movement of regulatory nodes change color etc e Reset Regulatory Factor Nodes Resets the regulatory factors and makes they aligned with the process nodes neatly Pathway Viewer Metabolism of glucocorticoids and mineral corticoids SEE File Tools Layout Actions Options Help SCH SGA RMAQ G Slr N BHR M Search for an Entity 11 deoxycorticosterone Delete Clear M Split Molecules
28. viewing gt List all genes involved in this process gt Pathway Folate pathway Organism unspecified Figure 16 The popup menu over an enzyme or a process node 18 Genomes Pathway Browser 2 0 metabolic pathways File View Query Web Resources Pathways Genes involved in this process or pathway a Z Folate 4 Formal a a S A S O g Processes 0425 serine hydroxymethyl ll Molecular transferase 1 soluble mnaman a M eR GR RMAQ G wara Synonyms of this molecular entity Genes viewing gt List all genes involved in this process Metabolic Pathways Explorer lt gt Signaling Pathways Pathway Folate pathway Organism unspecified Figure 17 The interaction between the upper right window of the pathway browser and the pathway viewer After clicking popup menu items the upper right window of the pathway browser displays the output table for the associated queries 3 3 Edge pop up menu options Figure 18 e Delete all bend points Delete all be points of this edge Make the edge a straight line Split the substrate or product node this edge connects to Splitting a node shared by multiple processes may improve the graphic representation This splitting can be done by heuristics and or under the direct control of the user This way the user can select to view the pathway with or without controlled redundancy The split molecules are added into the Split Molecules panel in the Common Molecules
29. ving inside the graph window Figure 24 illustrates selection in the overview window Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help SHER RMAQ GS B98 BDBHO COFEEEE A ae CELOEES a VA a S Z Z Z VA A Z A A A A A A Z A A A Z A y Z tttttttttttttt ti T prette Selected Graph Properti Biosynt amp Properties Comn 4 gt Pathway Biosynthesis of Riboflavin Organism unspecified Figure 24 The overview window and the main display window The overview window displays a rectangle to indicate the currently displayed area in the main active window Users can view larger portions of the graph by just stretching the square appearing in the overview window Also users can move view different portions of the graph by just moving the square inside this overview window to different areas Figure 25 illustrates with an example 25 Pathway Viewer Biosynthesis of Riboflavin FMN and FAD SEE File Tools Layout Actions Options Help SH S6QRMAQ GIS RBH Selected Graph Properti x Biosynt Nadas 20 x w gt I E Properties Cormn 4 gt Pathway Biosynthesis of Riboflavin Organism unspecified Figure 25 The overview window and the main display window The overview window displays a rectangle to indicate the currently displayed area in the main display window Users may resize the overview window and the inspector wind
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