Home

Vector PathBlazer 2.0 User's Manual

1. J Jz UTA d ix I ze Glycolysis Pathway Discovery unrestricted view Database lt _ Phosphofructo Glucose 6 phosphate isomerase E e US AGeinet B 3 H20 KO Fructose 6 phe Glucose 6 phosphate Glucose Master View Text View new For publication Current Database C Documents and Settings jill INFORMAXINC My Documents My PathBlazer Data PathBlazer PathBlazer_demo_db mdb Figure 3 29 New tab is added and default graphical properties display in new Alternate View 30 Working with Pathways Chapter 3 Copy a View by selecting the graphical view either the Master View or another Alternate View but not the Text View you want to copy and selecting Tool gt Manage Alternate Views gt Copy View Name the view in the dialog box that opens and click OK A new tab is added to the Graphics window either next to the Text tab or next to the last Alternate View that was added and looks exactly like the view from which it was copied To save the new view to the pathway click Save Delete an Alternate View by selecting the tab of the view you want to delete and selecting Tools gt Manage Alternate Views gt Delete View To save the pathway without the deleted view click Save The Master and Text View tabs cannot be deleted Working with Pathways in the Database Explorer The Database Explorer has several main functions including browsing database contents orga nizing
2. Figure D 3 Error generated when an attribute is incorrectly defined in the first entry Solution To determine where the source of the error is in the file look for any incorrectly defined attributes in the first entry of the file 207 Vector PathBlazer 2 0 User s Manual 208 Glossary mdb file Vector PathBlazer database file pw file Vector PathBlazer min database file that that stores individual pathways and associ ated reaction and component data Alternate View A copy of an existing view or a new view in the Graphics window that is saved with a pathway Components connectors or reactions in a pathway cannot be added or changed in an Alternate View but the graphical properties of the pathway elements and the graph can be changed Annotation A descriptive property of a component connector reaction or pathway such as name or cellular location Component One of the main database object types that is an element of a reaction Can be either an input or an output of the reaction and can be any kind of molecule such as protein DNA RNA or small molecule Can also be a physical element such as heat or light Connector Secondary database object type that links a component to a reaction node Can be unidirectional forward or reverse bidirectional catalytic or non directional protein protein interaction Discovery View Type of view where catalytic reactions those that involve an enzyme and a bidire
3. Interaction Catalysis E Activation Er Master View x z gt a All Reaction N ek Demo React Type EC 2 7 1 Common name Glucokinase Synonym Gluco GLC ATP gt CPD 222 ADP Type EC 1 1 1 Common name Gluconate 5 dehydrogenase NAD P GLUCONATE gt NAD P H SK GLUC Type EC 2 7 1 Common name Gluconokinase Synonym Gh ATP GLUCONATE gt ADP 6 P GLUCONATE are a daa b ia num Figure 5 20 Adding a reaction from the Database Explorer You can add only one reaction to a Graphics window using this method If you double click on a second reaction a new Graphics window opens You can add additional components by draw ing them from the Palette window or dragging them from the Database Explorer and then joining them to components in the reaction you opened You can also add reactions using the method described in the following section Adding an Existing Reaction from the Graphics Window Note Reactions can be added from the database that have a component in common with one you have selected in the Graphics window For example you might have opened the first reaction in glycolysis using the method described in the previous section and now you want to add the sec ond reaction that starts with glucose 6 phosphate without having to draw components and con nect them To add a stepwise reaction all reactions in the database or in one or more specified subs
4. ie ector PathBlazer 2 Glycolysis Pathway File Edit view Tools Layout Window Help A 7 a e KA La Expression Data Sets DeRisi Diauxic Shift D Expression Eure SARIO IROZ OIR olsy st e GUEURE Ue E ZG Glycolysis Pathway Discovery unrestricted view Database Physical Lipid DNA RNA Enzyme Protein Undefined BEE H20 i Normal Interaction Catalysis d Activation k Inhibition 4 Master View th Current Database C Documents and Settings jill INFORMAXINC My Documents My PathBlazer Data PathBlazer PathBlazer_demo_db mdb NUM Figure 8 21 Different expression runs can be displayed on pathway components Modifying Display Colors for Expression Value Ranges Use the following steps to modify colors for expression value ranges 1 Select Tools gt Options and select the Set Expression Data Ranges tab The tab contains the columns Start End and Color and initially contains the default values shown in Figure 8 22 set Expression Data Ranges Set Palette Pull Down Molecules 100000 OO Ga Add Edit Delete OK Cancel Help Figure 8 22 Expression Data Ranges tab for associating expression value ranges with display colors 2 To define a new range click Add to open the Expression Data Range dialog box Figure 8 23 Define the start and end value of the range in the Start Value and End Value fields 181
5. 101 Vector PathBlazer 2 0 User s Manual When you have completed the import the components and reactions relating to the imported file display in the Explorer List Pane with the PPI datasource listed in the Database Source col umn Similar to DIP and BIND PPI data contains only information about interactions between two components that is proteins There are no predicted products and each PPI reaction is repre sented as a protein protein interaction Importing Proprietary Data Proprietary data in the form of components reactions and pathways can be imported into the Vector PathBlazer database by formatting the data in an XML file according to the DTD Docu ment Type Definition for Vector PathBlazer The format of the XML file for proprietary data is the same XML format into which public data is automatically converted by the program for import into the database The complete DTD for formatting Vector PathBlazer XML files is provided in Appendix B An example XML file is provided in the following sections that you can use to format a proprietary file The XML file is made up of three main parts a list of substances that is components a list of the reaction or list of pathways Defining Components 102 The first part of the file contains a list of substances that is components and the attributes of each component For each component described between the lt substance gt attribute a compo nent object is created
6. 92 Importing Data Chapter 4 5 Select the root folder storing the multiple BioCyc files by clicking the Browse button Locate the corresponding file in the Browse for Folder dialog box and click OK The complete path to the root folder file displays in the Root Folder field Figure 4 11 PathBlazer Import EA Organism Escherichia coli Foot folder Browse Files Info lt Back Cancel Help Figure 4 12 BioCyc Import dialog box for selecting the root folder 6 In the Merge Options dialog box select the options appropriate for merging the data See Merge Option Dialog Box on page 67 for more information Click Next to continue The data loads while a monitor displays allowing you to follow the import progress An import log summarizing import results displays when import has been successfully com pleted Click Close 8 To import the data click Next The Load BIND dialog box opens and displays the progress of the import To stop the import click Cancel 9 A message displays when import is successfully completed Click Close BioCyc data includes components reactions or pathways so these objects will be distributed into all of these PathBlazer folders BioCyc is the only publicly available database with pathway objects Importing TransPath Data TransPath is comprised of molecules that participate in signal transduction and their reactions thus creating a complex network of interconnected sign
7. ATP H periplasm phosphate ADP 1 Z3799 MONOMER A component named putative ATP synthase beta subunit with the synonym Z3799 MONO MER will be created The reaction equation H cytoplasm H2O ATP H periplasm phosphate ADP and the subunit composition will be entered into the description field BioCyc Reaction Files Reaction files describe reactions They are parsed into reaction objects in the PathBlazer data base Some reactions described as a simple reaction in BioCyc files will be parsed into more then one reaction in PathBlazer For example an enzymatic reaction with an enzyme being acti vated by some other compound will result in two reactions in database one describing an enzy matic reaction by itself the other a reaction of enzyme activation The parsing of reactions starts from reactions dat Later non redundant information is added from files bindrxns dat and enzrxns dat File reactions dat This file contains general information about reactions The reaction is constructed from data stored in this file as well as from references made to other files of BioCyc 89 Vector PathBlazer 2 0 User s Manual The following is an entry from the reactions dat file UNIQUE ID R81 RXN TYPES EC 2 7 1 COMMON NAME Hexokinase EC NUMBER 2 7 1 1 IN PATHWAY ANAGLYCOLYSIS PWY IN PATHWAY P122 PWY LEFT GLC LEFT ATP OFFICIAL EC NIL RIGHT GLC 6 P RIGHT ADP SYNONYM Hexokinase type IV SYNONYM Glucokinase The fo
8. Component ATP Lipid B d DNA RNA o e Eo EA q Connector D D o r Reaction de Node ADP EE Protein EE Glucose 6 phosphate ee ee es A es a e a a ee ee E Undefined emen Master View Current Database C Documents and Settings jill INFORMASINCIMY Documents My PathBlazer DatalPathBlazer PathBlazer_demo_db mdb I MT aly Figure 3 7 Step 1 of glycolysis represented in the Graphics window 15 Vector PathBlazer 2 0 User s Manual 16 Each component connector and reaction is drawn independently of other elements in the Graphics window and each element can be moved independently and has its own graphical properties and physical attributes The graph itself also has its own graphical properties several additional examples follow showing how components and reactions can be represented in the Graphics Pane A B gt C Figure 3 8 shows a unidirectional reaction in which two substrates Mol A and Mol B react to form one product Mol C A separate arrow is drawn from Molecule A and Molecule B to the reaction node in a left to right direction showing that both of these two components or substrates are required for the reaction to proceed A single arrow is drawn from the reaction node to Molecule C in a left to right direction showing that it is the result of the reaction wiol A wiol wiol B Figure 3 8 Unidirectional reaction with substrates and product A B lt gt C Figure 3 9 shows a bidirec
9. b KA La Expression Data Sets None Expression Runs Roa OIR Ol Sly s J JB 7rulA S Sn Sa E New PathWay 1 Discovery unrestricted view Database DNA RNA al e E D rs Normal Interaction Glucose 6 phosphate t 4 Catalysis Gu Activation SE SA Master View Figure 5 18 Many components are joined into a reaction via a single reaction node 4 Continue adding components and connectors to a single reaction node or add additional components and connectors to form other reactions You can add multiple reactions to a pathway without joining each reaction in the pathway To connect two reactions into a path way join the ending or resulting component of one reaction with the starting component of the next In Figure 5 79 the first and second steps of glycolysis are joined to form a pathway via the component Glucose 6 Phosphate which then becomes part of two different reac tions Se Ze New PathWay 1 Discovery unrestricted view Database DNA RNA Gp Glucose Reaction 1 Enzyme Protein Undefined _ l H20 i Glucose 6 phosphate Fructose 6 phosphate Normal Interaction d ZE Glucose 6 phosphate isomerase Catalysis Reaction 2 Gu Activation bd SA Master View Figure 5 19 Joining two reactions into a pathway 5 When you form reactions using connectors the reactions are called lt UNNAMED gt by default and are not saved to the database automatically The pathwa
10. e One component at a time can be dragged from the List Pane and dropped into the Graphics window The Graphics window can either be blank that is a new Graphics window or can display one or more components reactions pathways or experiments Experiments display only when a pathway is open You can drag and drop more than one component into a single Graphics window but you cannot select multiple compo nents in the List Pane and drag them all into the window at once Use the instructions in Adding a Reaction on page 122 to connect a component to another component in a reaction or pathway Working with Pathways Chapter 3 Note If the component or reaction you are adding to a pathway or reaction is already present in the displayed pathway an Add Reaction dialog box opens displaying the duplicate object and allows you to resolve the issue in either of two ways Check the Pool checkbox to link the object with the existing reaction or pathway Check the Do not Pool checkbox to maintain the duplicate object in a separate reac tion or pathway in the Graphics Pane e Reactions and pathways can be opened in the Graphics window from the List Pane by either double clicking on a reaction or a pathway or selecting Open from the shortcut menu Each subsequent reaction or pathway that is opened from the Database Explorer is Opened in a new Graphics window To add reactions to a displayed reaction see Add ing a Reaction on page 122 To add comp
11. For more information about using Vector Xpression refer to the Online Help opend from Vector Xpression 3 1 or the Vector Xpression 3 0 User s Manual Searching a Vector Xpression Database From a specific pathway selected in PathBlazer 2 0 you can launch a search in Vector Xpres sion for a list of chips Expression Runs or Experiments containing genes coding for compo nents of the pathway To do so complete the following steps 1 From an open PathBlazer window in the Database Explorer select a pathway in a Path ways folder Right click on the pathway and select Search in Vector Xpression from the shortcut menu The Search Components dialog box that opens lists the components in the selected path way Search components in Yector Expression database EA Components 1 3 Bisphosphoglcerate 2 Phosphoglycerate S phosphoglycerate Dihvdroxyacetone phosphate Enolase e Use template veast Mapping E Vector Expression database ENT Database S peed Tutorial rd Browse Cancel Help Figure 8 15 Search Components dialog box for selecting options to search a Vector Xpression database 4 In the Use Template field select the template that is mapped to the expression objects linked to the listed components 5 Inthe Vector Xpression database field select the database to be searched 176 6 Working with Gene Expression Data Chapter 8 Click Search to execute the search Opening an Experim
12. Glycolysis Pathway File Edit View Tools Layout Window Help A e SE e x La Expression Data Sets DeRisi Diauxic Shift D Expression Runs 9 hours D So b Me B E a O y ZESTA d 33 Glycolysis Pathway Discovery unrestricted view Database Phosphofructokinase _ gt ROAR S x Physical ep Lipid E DNA RNA Enzyme Protein Fructose 1 6 bisphosphate Undefined BE H20 Normal Glyceraldehyde 3 phosphate dehydrogenase Interaction Catalysis 1 3 Bisphosphoglycerate b au Activation E Phosphoglycerate kinase duro Inhibition 4 Master View 7 Current Database C Documents and Geta INFORMAXINC My Documents My PathBlazer Data PathBlazer PathBlazer_demo_db mdb NUM ee Figure 8 19 Expression values display on enzyme components for Glycolysis in Discovery View 6 Pause the cursor over a component to display a tool tip that contains the component name the expression run name the gene name ID and the expression value Figure 8 20 slucose 6 phosphate isSOmerase Glucose 6 phosphate isomerase Expr Run 9 hours Poll 0 254936 Figure 8 20 Tool tip that display expression information about a component 180 Working with Gene Expression Data Chapter 8 7 Select a different expression run from the Expression Runs drop down list on the Graphics toolbar to display another set of expression values on the pathway Figure 8 27
13. Help Figure 7 9 Gene Ontology Annotations Import Options Gene Ontologies Chapter 7 The left panel GO db abbreviations displays abbreviations used in annotation files for standard biological databases For example SPTR is a frequent abbreviation for Swiss Prot but perhaps the abbreviation for Swiss Prot is different in another database Example Download the file sptr goa with SwissProt annotations from the Gene Ontol ogy Consortium website The menu will display the SPTR database abbreviation from the goa file mapped to the SwissProt link in PathBlazer The right panel of this dialog box Crosslink db displays abbreviations of databases to which there are cross links in PathBlazer The center panel in the dialog box allows you to verify or add abbreviations with their corresponding databases To add a term from the left or right panels select an item and click the Add button Once added to the center column select and add the matching abbreviation in the opposite panel 5 Click Next to continue During the import process of gene ontology annotations the annota tions are automatically associated with objects in the database you previously imported into PathBlazer To search the database for objects annotated with specific GO annotations see Search Data base by GO Annotation on page 61 Population of Organism Subcellular Location Attributes Based on GO Annotations GO annotations can be applied manually as described on
14. gt lt ELEMENT cell_ compartment item parts parts_location gt lt ELEMENT item NMTOKEN gt lt IATTLIST item Op CDATA REQUIRED gt lt ELEMENT parts NMTOKEN gt lt IATTLIST parts Op CDATA REQUIRED gt 192 DTD For Data Import Appendix B lt ELEMENT parts_location NMTOKEN gt lt ATTLIST parts_location Op CDATA REQUIRED gt lt ELEMENT stage NMTOKEN gt lt ATTLIST stage Op CDATA REQUIRED gt lt ELEMENT list_of_pathways_names pathway _name gt lt ELEMENT pathway_name PCDATA gt lt ELEMENT list_of_annotations annotation gt lt ELEMENT annotation HPCDATA gt lt ELEMENT list_of_reference_accesses db_reference gt lt l see origin_access gt lt ELEMENT db_reference type_of data database access item_URL extra_data gt lt ELEMENT comments PCDATA gt lt ELEMENT list_of_ formulas formula gt lt Description of formula gt lt ELEMENT formula SMILE gt lt ATTLIST formula expr CDATA REQUIRED gt lt ELEMENT SMILE PCDATA gt lt ELEMENT interaction list_of_origin_accesses creator create_date update_date list_of_hyperlinks synonyms type 193 Vector PathBlazer 2 0 User s Manual group _name list_of_subcomponents definition of _locations list_of_pathways_names list_of_annotations list_of_reference_accesses comments list_of_conditions list_of_diseases reversible effect confid
15. lt to delete the com ponent Bold type Options that you select in dialog boxes or drop down menus Buttons or icons that you click Example Click the Add button Italic amp bold type Text that you type Example In the New Subset text box enter Proprietary Proteins Note Highlights a concept of particular interest or information of Warning which you should be particularly aware Important Example Note This concept is used throughout the man ual Blue text that is underlined Hyperlinked text The hyperlinks can be URLs to Web sites Blue text italic font cross reference or they can be cross references within the user s manual hyperlinked in the Vector PathBlazer User s Manual pdf for easy reference Examples www informaxinc com Gene Ontologies on page 8 Table 1 1 Text conventions used in this manual CHAPTER OVERVIEW OF VECTOR PATHBLAZER This chapter provides a summary of how Vector PathBlazer provides a solution for managing pathway and protein protein interaction data and describes the database and key data types Topics in this chapter include e Main Features on page 5 e Vector PathBlazer Database on page 6 Pre Loaded Data on page 7 e Gene Ontologies on page 8 e Integration with Vector Xpression 3 1 on page 8 Introduction Biological science has surpassed the stage of cataloging simple parts and is facing the chal lenge of understanding a system s function the network of pro
16. lt synonyms gt tags An excerpt from the molecule xml file describing glucose is shown below The fields which are extracted are highlighted The lt comments gt and lt references gt tags are used to define crosslinks to other objects inside TransPath e g to reactions as well as to objects in external databases lt Molecule id MOQ000021249 gt lt Copyright c Biobase GmbH gt lt creator gt mkl lt creator gt lt updator gt mkl lt updator gt lt type gt other lt type gt lt name gt glucose lt name gt lt synonyms gt Glc lt synonyms gt lt comments gt lt item type Annotate xlink type simple xlink href annotate xml ID AN000031352 xlink show new xlink actuate onRequest gt ANO000031352 lt item gt lt comments gt lt references gt lt references gt lt Molecule gt File reaction xml This file stores information about reactions and references to components in molecule xml An excerpt describing one reaction is shown below The reaction will have the unique id XN000000001 Its formula will be GTP Ras GDP GEF gt Ras GTP GDP GEF plays an enzymatic role in this reaction Tags lt reactants gt lt products gt and lt enzymes gt contain refer ences to respective molecules in the molecule xml file lt Reaction id XN000000001 gt lt Copyright c Biobase GmbH gt lt creator gt frs lt creator gt lt updator gt frs lt updator gt lt type gt mechanistic lt
17. nents to which it is linked are saved with it For information about saving reactions see Saving PathBlazer Components Reactions and Pathways on page 46 When a component or connec tor is changed or deleted or when a component is added to a saved reaction you are prompted 127 Vector PathBlazer 2 0 User s Manual to either update create or disconnect the reaction from the pathway Table 5 3 describes each action Action Description Update reaction Makes the change to the reaction in the pathway and resaves the reaction under its original name when the pathway is saved This option is only available when the reaction does not participate in more than one pathway in the database This option is also only available when an added component already exists in the database Create new reaction Makes the change to the reaction appends the name of the reac tion with an incremental number and saves it as a new reaction in the database when the pathway is saved The new reaction takes the place of the original reaction in the pathway Any annotations that were present in the original reaction are retained This option is only available when an added component already exists in the database Disconnect this reaction from Makes the change to the reaction but disconnects the current pathway reaction from the pathway and adds an unsaved reaction to the pathway called lt UNNAMED gt Also any annotations in the original reaction are
18. 1 The Master View tab is for viewing the elements of a pathway graphically see Viewing Pathways Graphically on page 14 2 The Text View tab is for viewing the elements in text format see Viewing Pathways in Text Format on page 28 FSi Vector PathBlazer 2 Glycolysis Pathway O O lol x Graphics File Edt view Tools Layout Window Help E Toolbar pen E e La z e x La Z Expression Data Sets None D Expression Runs R Soa af ho ir a EK EEE EE EE E AES AE A A A a A B E ZO EE Palette EHE Da Window 0 ADP DNA RNA Glucose 6 phosphate Enzyme Ee Glucose 6 phosphate Na Protein isomerase EO Undefined a ps Fructose 6 phosphate Graphics Window Normal Phosphofructokinase durra Interaction Fructose 1 6 bisphosphate Catalysis gt Activation E Aldolase Inhibition Master Text e Views Tabs Master View Current Database C Documents and Settings jill INFORMAXINC My Documents My PathBlazer Data PathBlazer PathBlazer_demo_db mdb Num a Figure 3 3 Elements of Pathway Viewing Area The Palette window is anchored on the left side of the screen by default but can be converted to an independent window by dragging on the double line on the top of the window and dropping it when its borders retract to a smaller rectangle The window can then be dragged anywhere on the screen To reanchor it on the left side of the screen again drag it to the left and drop it when i
19. 42 Tab Screen Crosslinks cont d Locations URL Type URL Tissue Organelle Description Fully qualified URL Value s Example http www expasy org cgi bin get enzyme entry 5 4 99 3 String Note When KEGG BIND TransPath BioCyc and DIP entries are imported one or more URLs is automatically created for entries in these databases For more information see Pre Defined URLs on page 107 Designates how definitively it is known if an object is present in a location Values Known in Not in In See definitions in Organism field Designates which tissue an object is known to occur in String Designates which organelles an object is known to be in Values cell wall centriole centrosome chloroplast chromatin cilia cis golgi cytoplasm cytoplasmic mem brane cytoskeleton endosome ER general ER rough ER smooth extracellular flagella Golgi golgi stack lysosome medial golgi mitochondrion nuclear pore nucleolus nucleus nucleus inner mem brane nucleus outer mem brane outer membrane peroxisome plastid ribosome trans golgi vacuole vesicle Pathway P Reaction R Component C Table 3 5 Annotation fields and values for pathways components and reactions Continued Working with Pathways Chapter 3 Pathway P Reaction R Component C Tab Description Screen GEO Value s GO Annota Source Data Original source of the term or the anno
20. El Uze template Yeast Mapping PathBlazer database JED ocuments and Settings INFOR MASING My DocumentssMy F Browse Cancel Help Figure 8 16 Save Experiment dialog box for selecting PathBlazer database for expression data sent from Vector Xpression Click Save The Experiment will now be included in the Experiments folders displayed in the PathBlazer Database Explorer Finding Components in PathBlazer From Vector Xpression 3 1 you can launch a search in PathBlazer to find components mapped to expression data in Vector Xpression To do so complete the following steps 1 In the Vector Xpression Database Explorer select Expression Genes from the Tables drop down list and then select the gene s that you want to map 177 Vector PathBlazer 2 0 User s Manual or Open an Expression Runs Viewer Runs Project Viewer or Experiment Viewer displaying data with genes that you want to map Select the gene s that you want to map 2 Select Tools gt Find Components in PathBlazer If you have selected genes from a list you can choose the option to search for all the listed genes or only the selected genes 3 Inthe Search Genes in PathBlazer Database dialog box that opens the selected genes are listed In the Use Template drop down menu select the mapping template where the com ponents are mapped 4 In the PathBlazer Database drop down menu select the PathBlazer database to be searched 5 Click S
21. H20 Normal Interaction x _Master View ZI AIS HE EEE TE EEK EO Mol weight 178 141 SMI C6H1006 1 9 2004 9 23 43 AM d Catalyzes ATP glucona 1 9 2004 9 24 09 4M ea SG molecule 12 2 2003 3 16 45 PM a galka Ga Mol weight 259 152 SMI C6H14NO8P 1 9 2004 9 23 43 AM Catalyzes H20 D gluco 1 9 2004 9 23 32 AM Gi intersection d 12 2 2003 3 16 44 PM GUO 12 2 2003 3 16 45 PM SMM E Figure 5 16 Adding a component from the Database Explorer section to link components into reactions Adding a Reaction Similar to components reactions can either be drawn de novo or existing reactions can be added from the database You can add an unlimited number of reactions to a single pathway and each reaction does not necessarily have to be joined together For example you might want to represent all of the protein protein interactions in a pathway from the BIND database where each interaction is not necessarily linked to a subsequent interaction Instead the pathway is made up of a number of separate protein protein interactions Drawing a New Reaction Components are joined into reactions by connectors which are represented as lines in the Pal ette window At least two components must be present in the Graphics window before a connec tor can be added Use the following steps to join components into reactions 1 If there is only one component in the Graphics window add at least one m
22. Vector PathBlazer 2 0 User s Manual 182 The Start Value is defined as greater than or equal to gt and the End Value is defined as less than lt Assign a color to this range by clicking the Browse button in the Color field Select a color from the palette and click OK Click OK in the Expression Data Range dialog box Expression Data Range EA Stark value m End yalue f Color PTE 3 Cancel Figure 8 23 Dialog for defining range values and colors Add additional ranges by repeating the instructions in step 2 Edit a color or range by select ing the definition clicking Edit and making the change in the Expression Data Range dialog box Delete a definition by selecting it and clicking Delete Continue to the next section to display expression data on pathway components by the associated color and range APPENDIX LICENSE MANAGER Once you have installed Vector PathBlazer you will need to license the application to be able to use it To satisfy the needs of users in different industrial scientific or educational environments Invit rogen has designed four types of Vector PathBlazer licenses These are all administered through the License Manager e Static License Purchased by one user for installation on one computer e Dynamic License DLS A license that is installed on a server and issued by that server to client Vector Advance computers DLS licenses are shared by a specified number of users
23. step 1 e B in two steps in the backward direction then only the one step pathway Is returned because the program goes against the direction of the connectors from B to A e Bin two steps and ignore direction then the following pathway is returned in which direc tions is not considered ge E SEE E Sep 2 Specify the forward direction by selecting Forward from the drop down list in the Direction field Specify the backward direction by selecting Backward from the drop down list Specify no direction by selecting Ignore from the drop down list Interaction generality refers to protein protein interactions It is defined as the number of pro teins that directly interact with the target protein pair minus the number of proteins interacting with more than one protein plus one In general the lower the generality score the more biolog ically relevant a protein protein interaction Protein protein interactions extending from a specific protein that have an interaction generality score lower than that set will be used in the assembly of the protein protein interaction network Interaction generality is undefined for interactions with more than two components Build a network of protein protein interactions by selecting Ignore from the drop down list 137 Vector PathBlazer 2 0 User s Manual Set the interaction generality score by selecting a value from the drop down list in the Inter action Generality field The default sett
24. 0 9716996 1 94046466 2 17512417 155209202 BEIZ O 04255 O 065083 0 50516176 O 69984198 0 5571909 0 62666r702 0 14575446 sPM2 O 010229535 0 106847524 0 43966141 1 10085951 126455126 1 35017373 1 53552413 TFI 00 0605137 0 1218064 0 12004598 0 22056738 0 12276019 0 63175696 0 4548502 HEK O2554089 O 179 4054 0 22622936 0 02555606 UL ZI ZARIA 1 6666r7346 1 69504555 SDH4 0 0759175 O lt 05501215 0 46203597 1 0740426 107697654 2 50559942 3 00795627 Hak 0 13350231 044254444 2955609 1 11925592 1 61669544 3 00111532 0 5344425 Hak O 57024054 0 51907164 026144058 0 10900465 0 218679733 O 1590258 0 6 750557 TOH3 GUIE TZIO 0 0051946 O253501776 0 3055166 0 26721619 0 56369326 UL ZEA PZO EDS 0 2090392 0 06337 ZO 0 22325653 0 16373081 0 16994701 UL 4627955 0 41596639 FFK 0 14053964 UL 4442r UL IEE OU 0 0490269 JUAGU 0 4541662 0 325604 LSC 0 16556155 0 29050536 067035093 1 16666527 I 69606021 25427947 2 36182714 ENGO 0 0167263 O 02121205 0 05796847 0 14575298 01606347 0 55775420 00 0124604 ENO 0 049061 0 145198 O 02e65794 0 066697 46 0 31022173 0 09760213 0 5004593 UGO 0 19573702 046567350 025117495 0 29444945 06933944 1 66465735 3 4025570 TOHI 0 02239369 0 16103742 0 53612065 O 46562798 0 5220232 0 85403061 0 01175296 TOH2 0 0669973 0 0156736 0 0125664 0 076479 0 26498613 0 55451679 0 15162939 FEA U 0025821 UL UZEI 0 1566256 UDUAUZZ ULI ZARATE OSOS6609S 0 5619637 MDH1 0 02102616 0 09521656 O 165566835 1 09546307 1 55207337 AIEI I
25. 19 2004 Component dinI renamed into dinI Cdupl 1 Component recA renamed into recA Cdupl 1 Merging component S adenosyl homocysteine into S Adenosyl L homocysteine Component BIZ renamed into ble dupl 1 Component GI renamed into SBI dupl 1 Component trpL renamed into trpl Cdupl 1 Component TAO renamed into fadD Cdupl 1 Merging component NAD into NAD Component crp renamed into crp dupl 1 Merging component NADP into MADE Activity Import wed Jan 28 12 36 12 2004 Activity Import wed Jan 28 12 48 02 2004 merging component dini into dinI dupl 1 conflicts found while merging component AMP into AMP Organism contradiction Known In E coli H 0157 dropped because of only In E coli merging component recA into recA Cdupl 1 conflicts found while merging component NH3 IDEO NEZ Organism contradiction Known In E coli H 0157 dropped because of Only In E coli merging component S adenosyl homocysteine into S Adenosyl L homocysteine conflicts found while merging component co2 into co2 Organism contradiction Known In E coli H 0157 dropped because of Only In E coli conflicts found while merging component NADPH into NADPH Organism contradiction Known In E coli H 0157 dropped because of Only In E coli Merging component blc into ble dupl 1 Merging component c
26. 41 Xenarios Salwinski L Duan XJ Higney P Kim S and Eisenberg D 2002 DIP The Database of Interacting Proteins A Research Tool for Studying Cellular Networks of Protein Interactions Nucleic Acids Research 30 303 5 201 Vector PathBlazer 2 0 User s Manual Licensing Information Academic users may freely download DIP data Registration is required at_http dip doe mbi ucla edu dip Login cgi R 1 Non academic users must obtain a license For more information see hitp dip doe mbi ucla edu dip Login cgi R 1 Pre Loaded Data Metabolic Pathways Glycolysis Gluconeogenesis and TCA Cycle Lehninger AL Nelson DL and Cox MM Principles of Biochemistry Worth Publishing 2000 Third Edition Pentose Phosphate Pi Pathway Stryer L Biochemistry W H Freeman and Company 1995 Fifth Edition Signal Transduction Pathways EGF TNFR Wnt Schoeberl B Eichler Jonsson C Gilles ED and Mueller G 2002 Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors Nature Biotechnology 20 370 75 Chen G Goeddel DV 2002 TNF R1 Signaling A beautiful pathway Science 296 1634 35 Moon RT Bowerman B Boutros M and Perrimon N The promise and perils of Wnt signaling through beta catenin 2002 Science 296 1644 46 Gene Expression The expression data described in Chapter 8 was obtained from the article referenced below A tab delimited text file
27. Chemical Abstracts Service registry number Some of these attributes are imported into Vector PathBlazer as component attributes In the Vector PathBlazer database a separate object that is a component of which the type is Undefined is created for each KEGG compound listed in the file 1 ftp ftp qenome ad jp pub kegg ligand ligand doc 13 Vector PathBlazer 2 0 User s Manual The following is an example of a partial Compound file as it appears in a text editor Each entry starts with the ENTRY field and ends with the characters I Not all of the fields in the file are imported to the database The values shown in bold are parsed into an annotation field for the corresponding component Table 4 2 contains a mapping of the fields that are extracted by the importer a field description and where the value of the field appears in Vector PathBlazer for a component object ENTRY C00469 NAME Ethanol Ethyl alcohol Methylcarbinol FORMULA C2H6O REACTION RO0746 R00754 RO2359 RO2682 R04410 RO5198 R05208 PATHWAY PATH MAP00010 Glycolysis Gluconeogenesis ENZYME 1 1 1 1 1 1 1 2 1 1 1 71 1 1 99 8 DBLINKS CAS 64 17 5 A Component Annotation in Vector PathBlazer Field Name Description Name The recommended name of the Name compound and any alternative First entry is imported as the primary name to names The recommended the Name field This name is the primary name name is the first name or the unique identifier in Vector P
28. Data to PathBlazer on page 177 e Youcan launch a search in PathBlazer for components that map to expression objects in Vector Xpression See Finding Components in PathBlazer on page 177 Linking Gene Expression Data to Pathway Components In Vector PathBlazer you can map expression data to pathway objects in PathBlazer either automatically recommended where possible or manually Mapping the two databases is gen erally based on the gene names used in Vector Xpression or other expression data files and component names or component database links in PathBlazer Links are saved as templates that can be used to import expression data files that have corresponding gene names You can edit the mapping templates by adding additional components or deleting components You can also share templates with other colleagues who are also using Vector PathBlazer or import PathBlazer templates for your use Any pathways to which the template file applies that is any pathways that have components in common with the gene to component mapping can have expression data displayed on them Creating an Template Automatically 166 To create a template automatically associating gene names with pathway components use the following steps 1 In Vector PathBlazer select Tools gt Manage Expression data gt Create Expression Tem plate 2 Inthe first screen of the Create Template Wizard select the PathBlazer database to which expression data will be mapp
29. Edit dialog box that opens Figure 7 7 change current information or add new information organisms are listed in their order of most frequent usage highest to lowest Once you click OK the fields display in the appropriate text boxes on the GO Annotations tab Edit GO Annotation E x Source DB Unique ID in DB Evidence Type Traceable Author Statement best D Organism D Dictyostelium discoideurn d Drosophila melanogaster Escherichia coli b Hepatitis C virus Homo sapiens Figure 7 7 Edit GO Annotation dialog box Delete a gene ontology annotation by selecting the bottom leaf on the annotation tree on the GO Annotations tab and clicking Delete The annotation is removed from the object but not deleted from the imported GO Annotations file Each GO annotation can have the following attributes e Source Database the database from which the GO term originates e Unique ID in database the ID in the original database e Evidence type the hierarchy of evidence or confidence in the validity of the annotation e Taxonomy ihe organism from which the term or annotation originated Updating GO Categories Note After you have downloaded gene ontology files from the Gene Ontology Consortium website and imported them into Vector PathBlazer you will need to return to the GO website http www geneontology org for periodic updates to your ontologies When GO categories are imported a second time updated all obsolet
30. Mapping options section select from the following radio buttons Use Gene Name gene names are compared with the name of component If they are the same mapping occurs Use Alternative Name alternative names synonyms of a component are used for mapping Use Foreign Key if the expression file has foreign keys from external databases such as Swiss Prot and the component in PathBlazer has a reference to the same object in an external database they can be mapped For example if a PathBlazer component is 167 Vector PathBlazer 2 0 User s Manual T crosslinked to the Biomolecular Interaction Network Database BIND via an accession number and that accession number is entered in a user defined field of a gene in the Vector Xpression database you can create a foreign key linkage in the template If you select the Foreign Key option Select the external database from the PathBlazer Cross link Database Name drop down list This list includes all the external databases with crosslinks to the selected PathBlazer database Select a column name in the Vector Xpression database from the Expression UDF Name drop down list that contains the linking values to the external database If this column contains multiple foreign keys you can select or specify a delimiter such as semicolon or comma or type in a custom delimiter such as In the Template Name text box enter a name for the template being created To replace or add t
31. Merging Components Manually Components and reactions are automatically merged during data import This automatic merge is not infallible however Source databases utilize different data models different substance classifications etc and it is inevitable that some components which should be merged will not be while others will be merged incorrectly All merge events are recorded in a log file described on page 71 If two components are merged incorrectly during import you can manually re create a missing component and link it to appropriate reactions There is no automatic way to un merge two components After data has been imported into Vector PathBlazer you can manually merge components using a Merge Wizard Use the following steps to manually merge components 1 Select one component in the List Pane of Database Explorer and select Merge Compo nents from its associated shortcut menu In the Merge Components dialog box that opens Component 1 displays the component you selected For Component 2 browse and locate a component in a subset Click Next to continue In the second screen of the Merging Components dialog box unique attributes of both com ponents are listed Select attributes that are to be included with the final merge product Attributes that can be selected are Name Chemical Formula Source and Component Class Click Next to continue The next dialog box lists non unique attributes as text strings whi
32. PathBlazer and Vector Xpression 176 Creating a Template from Vector KOTSSSIOOA laa 176 Searching a Vector Xpression Database atea 176 Opening an Experiment in Vector Xpression rra 177 pendine Expression Data AUE Ea 177 Finding Components in PathBlazer sa IK Displaying Expression Data on Pathways ss 178 Default Display Colors for Expression Values ss 179 Modifying Display Colors for Expression Value Ranges aa 181 Appendix A License Manager dE 183 License Manager Dialog BOX granate Eate ritate 184 Appendix B DTD For Data Import udak kaketa enak EE 191 Appendix C SS Si dal Le 199 Edesa AAE 199 REAN 199 TG CaP LOMA AAA 199 BIRA ENE 199 REPIC S s AEE 200 IBI RUA arai erea EE 200 LEN iD ater re merece men cere daget AD 200 IDESCHIPUON Aaa aaa aaa ate 200 RA EEA 200 RELE NCES aA Eee 200 Table of Contents Licensine areara AEE 200 BOC AEE 200 IOS CHIP E AAE 200 biba EAE 200 Uraren GA 200 icense Maiaga AAE 200 POMS AU AAE 201 TSSOP CLO PAA 201 URE gt 201 EE zarea aak eaz 201 LACENSIMO Oai 201 BEARRA eat testes ete ee ai tae teehee 201 ERRITAR 201 ISa BAA 201 Heart aak AEE 201 IB arabiera EEA 202 Pres berala Data AAA 202 Metabolic NOON 202 SERGE EEN brageta akara iatea aa 202 Gene ga ieta a EAEE 202 lateracho Eu ASA 202 Appendix D Troubleshooting MOA 203 GERTAT gata ieta eatea agata 203 OPOE sonr EE EOE ESA 204 OSS II Y arn eee ec eee ee eee ee 209 Lala ZA AAE 211 vii Vector PathBlazer Use
33. PathBlazer are e normal forward or reverse Overview of Vector PathBlazer Chapter 2 e interaction protein protein interaction e activation e inhibition e catalysis Reactions can be of the type characteristically described in metabolic or signal transduction pathways and have a defined direction as well as substrates and products or can be protein pro tein interactions which consist of two interacting proteins without a defined direction Similar to components reactions can have attributes associated with them such as cellular localization formula type etc Pathways are one or more sets of reactions linked together through at least one component Different types of pathways can be modeled in Vector PathBlazer including metabolic and signal transduction pathways Pathways can also be made up of networks of protein protein interac tions Similar to components and reactions pathways can also have attributes associated with them Experiments Gene expression data can be stored in the PathBlazer 2 0 database as Experi ment objects Experiments are composed of expression values obtained from genes that make up Expression Runs Experiments expression values map to PathBlazer database Compo nents upon import If expression data were sent to PathBlazer directly from Vector Expression Experiments the objects also retain reference to the original Vector Expression database Through the use of these four main data types you can
34. String Chemical For Chemical formula of a component mula Example C10H15N5010P2 ADP String Table 3 5 Annotation fields and values for pathways components and reactions 39 Vector PathBlazer 2 0 User s Manual 40 Tab i Description aaway ZO Screen Field Value s Reaction R Component C General Source Derivation of a component Component Values cont d Biological Synthetic Formula Formula of a reaction Example Chloroacetic acid H2O lt gt HCI Glycolate String Type Type of a reaction Values Generic Signal Transduction Metabolic Unknown Confidence Description level of confidence in this reaction Values Theoretical guess Unlikely Probable Possible Universally accepted Validity Significance of a path way Values Unknown Hypothetical Doubtful Novel Experimental Test Universally accepted Organisms Type Designates how definitively it is known if an object is present in an organism Values In Definitively known to be in one or more organisms If an object is in one or more organ isms all others are excluded Known in Known to be in an organism but all others cannot be ruled out Not in Opposite of Known in Known not to be in an organism but all others cannot be ruled out Table 3 5 Annotation fields and values for pathways components and reactions Continued Working with Pathways Chapter 3 Tab i Description Paway SO Field Reaction R Screen Value s B Component
35. Terms on page 154 After you have downloaded the Gene Ontology Annotations dictionary from the Gene Ontology Consortium website see ntroduction to Gene Ontologies on page 153 you can import the GO annotations file into PathBlazer Because gene ontology annotations are imported and stored in a PathBlazer database if you import them into one database and later switch to another you will have to repeat import of the Gene Ontology itself and Gene Ontology annotation file in the new database Use these steps to import gene ontology annotations 1 2 3 4 Open PathBlazer Select Tools gt Manage Gene Ontology gt Import Gene Ontology Annotations In the first Gene Ontology Import dialog box that opens click the Browse button to locate and select the GO annotations file you want to import Figure 7 8 Click Next Select source file JEAWNTINGO files sptr goa Browse Cancel Help Figure 7 8 Gene Ontology Import Gene Annotations dialog box The second Gene Ontology Import dialog box displays ontology related database informa tion Figure 7 9 Use this dialog box to map the abbreviations used in GO annotation files to abbreviations present in the current PathBlazer database GO DB Abbreviations SPTAR DB Abbreviation Crosslink DB SPTR SwissProt http iecb med harvard ed KEGG Klotho LIGAND LIGAND CPD Read all lt Back Cancel
36. UserPPI UserPPI UserPPI BIND BIND BIND UserPPI PPI role Trapped protein i PPI role Trapped protein i PPI role Trapped protein i PPI role Trapped protein i Mol weight 161 2 SMILE Catalyzes L carnitinyl Co PPI role Trapped protein i Probable component of se putative plasma membran sphingoid long chain base PPI role Trapped protein i C7H15NO3 Current Database C Documents pr Settings jill INFORMAXINC My Documents My PathBlazer DatalPathBlazer PathBlazer_ demo EES mdb Figure 3 4 Elements of Database Explorer Similar to the Palette window the Database Explorer window is anchored at the bottom of the screen by default but can also be converted into an independent window by dragging on the double line on the far left and dropping the window when it its borders retract to a smaller rect angle The window can then be dragged anywhere on the screen To reanchor it at the bottom of the screen again drag it to the bottom and drop it when its borders expand to fill the bottom or double click on the its title bar to return it to the bottom To close the window click the x in the upper left corner To view the Database Explorer window again select View gt Explorer Pane Menu Bar and Toolbars Menu commands and toolbar buttons are described throughout this chapter according to their use in the program Working with Pathways in the Graphics Window Before learning how to draw an
37. Vector PathBlazer 2 0 User s Manual Buttons Table 3 4 describes the actions of the buttons in the Layout Properties dialog box Saves any setting changes to the layout applies it to the pathway in the Graphics window and closes the Layout Properties box Cancel Cancels any changes to the settings returns the settings to previous and closes the Layout Properties box Help Opens a help topic appropriate for dialog box options Reset Returns settings to previous Applies the current settings to the pathway in the Graphics window Defaults Returns the settings to the default settings Table 3 4 Button actions in the Layout Properties dialog box Viewing Pathways in Text Format Note 28 In addition to displaying pathway elements graphically on the Master View tab you can also display them in text format by clicking the Text View tab at the bottom of the Graphics window The Text View tab provides a text summary of all the reactions connectors and components in a pathway as well as the annotations added to each Information in the Text View tab is orga nized in hierarchical folders and when you first click on this tab the Pathways folder displays with any objects selected in the Graphics window simultaneously selected in the Text View tab When viewing a pathway in the Text View tab the graphical tools in the Palette window and the Graphics toolbar are not available To view the contents in each folder click the sign to e
38. View any enzymes included in the results display as labels of the reaction in which they participate and are not pooled The Build a Pathway dialog box consists of several areas with different parameters in each Each area of the dialog box is described in the following subsections Following these descrip tions several scenarios are presented for building a pathway using different sets of parameters Build a Pathway Ee EZ EA Fath Build Pathway la from Component from Pathway Component Subsets T Ignore Paths through these Components Glucose Browse T Small Molecules Build Pathway IY to Component I to Pathway I Dont Pool Components in Subset pyruvate Browse GT All Components I Build Pathway through Component I Hide these Components A Choose Component Subset Include Reactions from Subsets I Show only connecting components Calculate critical points Connection Length Pathway Direction Maz Number of Steps Extra Steps Direction Interaction Generality f A E fo E Forward b E Unlimited e a Cancel Hep Figure 6 1 Build a pathway dialog box Selecting Components and Reactions 134 To create a meaningful pathway you should create pathway component and reaction subsets before you configure a query to automatically generate a pathway Subsetting effectively groups components pathways and reactions that are likely to participate in a pathway Components can then be quickly select
39. a New Component on page 113 or Drawing an Existing Component on page 118 To save the change see Saving PathBlazer Components Reactions and Pathways on page 46 To cancel the change and revert to the previous pathway close the pathway with out saving it and then reopen it Adding Selected Components or Reactions to a Subset To add components or reactions you have selected in the Graphics Window to a subset select the objects then right click anywhere in the Graphics Pane e To save to an existing subset select Append Selected Components Reaction to a Subset In the Append to Subset dialog box that opens select the subset to store the components reactions e To save the objects to a new subset click Save Selected Components Reactions as a Subset The dialog box is similar to the Append to Subset dialog but text boxes are available for you to name create and describe the new subset Click Append or Create to execute the command Deleting Components in a Reaction When components are deleted from a saved reaction a dialog box displays listing each reaction in which a component participates The difference between deleting and adding components is that once a component is added to a pathway it can participate in more than one reaction for example it can be a substrate in one reaction and a product in another During deletion actions can be applied independently to each with the same options To delete a component from
40. a saved reaction use the following steps 1 Select the component in the Graphics window and click the Delete button on the Graphics toolbar or press the DELETE key The dialog box in Figure 5 26 displays If the component participates in more than one reaction each reaction displays in a different row Each reac tion s name displays in the Reaction column ector PathBlazer 4 a X A Completing this action will affect the following reactions which already exist in leE Elte nl iE E a E EA E E E S Please select the action to take for each reaction d EEE d Figure 5 26 Dialog box that displays when deleting a component from a saved reaction Drawing Pathways Chapter 5 2 For each reaction select an option from the drop down list in the Action to take column Note see Table 5 3 for action descriptions If a reaction participates in more than one pathway the option Update reaction is not avail able Click OK The selected action is applied to each reaction listed To save the change see Saving PathBlazer Components Reactions and Pathways on page 46 To cancel the change and revert to the previous pathway close the pathway with out saving it and then reopen it Changing or Deleting Connectors in a Reaction A change to a saved reaction is also triggered when a connector s annotations are changed or when a connector is deleted To change a connector s annotations or delete a connector in a saved reaction
41. are saved using the Save command A wizard similar to that used for saving components is used to save pathways and reactions Pathways and reactions are saved as independent objects but are saved using the same wizard Saving a Pathway or Reaction to the Database or a File 46 To save a pathway all components must be connected to at least one reaction However sepa rate reactions in a pathway do not have to be connected to another reaction or do not have to be saved as part of a pathway Use the following steps save pathways and reactions 1 Select File gt Save or click the Save da button on the toolbar If the pathway has already been saved any changes will overwrite the existing pathway To save a pathway that has not been previously saved or to save the pathway under a differ ent name select File gt Save as The Save dialog box opens and includes a number of options Figure 3 39 Save Pathway i e x d Pathway b Save as new pathway Save ko Organisms Select a Subset Locations Reference Database bi All Pathways Cross Links File Name Reaction uro aro is d Components a A Properties Constants Name Reaction gluco rnd Conditions Datasource Organisms Locations Validity Unknow E Cross Links A Pathways Disease Complete b P Description Cancel Help Figure 3 39 Dialog box for saving pathways and reactions Important Working with Pathways Chapter 3 The Save
42. component 141 link between two pathways 149 showing connection from other datasources 150 through a component 145 C Circular layout applying 24 description 24 properties 25 Colors expression values in Graphics window 179 in automatically assembled pathway 138 modifying expression value display 179 Color schema applying universally 21 creating 21 Commonly used molecules adding 112 deleting 112 description 111 editing 112 Component adding to Graphics window 113 annotation fields 39 changing display name 113 commonly used molecules 111 copying 33 deleting 33 deleting from saved reactions 130 description 6 displaying database crosslinks 52 hiding in Graphics window 19 joining into reactions 122 renaming 33 viewing graphical properties 19 viewing in Text View 29 viewing properties 29 Components merging manually 45 Connector adding in Graphics window 122 annotation fields 44 changing in saved reactions 131 deleting from saved reactions 131 description 14 direction 45 hiding in Graphics window 19 211 Vector PathBlazer 2 0 Users Manual joining components into reactions 122 navigating in Graphics window 18 viewing graphical properties 19 viewing in Text View 29 viewing properties 29 Copying Alternate Views 31 Creating Alternate View 30 component subsets from reaction pathway 35 database 10 empty subsets 34 folders 34 reaction subsets from pathway 35 subsets 34 subsets with contents 34 Crosslinks defining ann
43. data and selecting data for display in the Graphics window Browsing Pathway Data In Vector PathBlazer there are two kinds of containers that you can use to organize data fold ers and subsets Each main data type that is Pathways Reactions Experiments and Compo nents in Vector PathBlazer displays in a folder in the List Pane the left pane of the Database Explorer Each main folder contains a subset called the All Component Reaction Experiment Pathway subset A subset is a type of container that contains references to objects in the data base and can be used to group objects with one or more properties in common The All Compo nent Reaction Experiment Pathway subsets are system defined subsets that reference each object of that type in the database Any number of user defined subsets can be created to orga nize objects Browse data containers by clicking the forward and backward 4 arrow buttons on the Database Explorer toolbar Move up a folder by clicking the folder button ta Folders and subsets display in the List Pane on the left of the Database Explorer and the objects they con tain display in the Contents Pane on the right Objects in the Contents Pane either display as a list with details about each object or simply a SZ on the Database Explorer toolbar to list the objects in the List Pane Click the Details button IESU to list properties of the objects in columns in the List Pane The columns N
44. dd Glucose 12 2 2003 3 16 44 PM ZL edo com 4 Glucose 1 phosphate INMX 12 2 2003 3 16 45 PM E beatza e diu Glucose 6 phosphatase 12 2 2003 3 16 44 PM e E E Glucose 6 phosphate 12 2 2003 3 16 44 PM SI ean uu de Glucose 6 phosphate dehydrogenase B 1 12 2 2003 3 16 45 PM ee i k 4 gt Current Database C Documents and Settings jill INFORMA4XINC My Documents My PathBlazer Data PathBlazer PathBlazer_demo_db mdb l NUK DO Figure 5 17 Connecting two components into a reaction Note The cursor remains a wand until you either click another shape or line in the Palette window click on one of the buttons in the Graphics toolbar such as the arrow icon e or press ESCAPE 3 When multiple components are involved in one reaction additional components are linked directly to the reaction node You can think of the reaction node as a hub where one to many components can lead into it and one to many components can result from it For example when hexokinase mediates the transfer of a single phosphate from ATP to glu cose to form glucose 6 phosphate and ADP all of these components lead to or result from the same reaction node Therefore once the first two components are drawn to create a reaction node the remainder of the components can be drawn to the reaction node itself Figure 5 18 123 Vector PathBlazer 2 0 User s Manual MS vector PathBlazer 2 New PathWay 1 4 7 E la x File Edit view Tools Layout Window Help A X E
45. group_ name list_of_subcomponents definition_of_locations list_of_ pathways _names DTD For Data Import Appendix B 195 Vector PathBlazer 2 0 User s Manual 196 list_of_annotations list_of_reference_accesses comments list_of_conditions list_of_diseases reversible effect confidence_level BioNet validity gt lt ATTLIST pathway ID ID REQUIRED gt lt ELEMENT validity universally accepted novel hypothetical doubtful experimental test dummy gt lt ELEMENT BioNet list_of_agents list_of_actions list_of_arcs gt lt ATTLIST BioNet ID ID REQUIRED gt lt Description of Agent gt lt ELEMENT list_of_agents agent gt lt ID should be unique into current BioNet only gt lt ELEMENT agent role substance_ref gt lt IATTLIST agent ID ID REQUIRED gt lt ELEMENT role educt product catalyst inhibitor intermediate none gt lt IDREF reference to substance placed into list_of_substances gt lt ELEMENT substance_ref substance gt lt ATTLIST substance_ref ref IDREF REQUIRED gt lt Description of Action gt lt ELEMENT list_of_actions action gt lt ID should be unique into current BioNet only gt lt ELEMENT action interaction_ref gt lt IATTLIST action ID ID REQUIRED gt DTD For Data Import Appendix B lt IDREF reference to any kind o
46. gt and select one of the submenus Metabolic Pathway or Discovery Pathway You can also click the New Pathway button KI on the toolbar and select from one of the submenus off of the drop down menu next to the button 2 A blank Graphics window opens that is labeled at the top of the window with either New Pathway1 Metabolic restricted view Database or Discovery unrestricted view Database Database indicates that the pathway is stored in the Vector PathBlazer data Drawing Pathways Chapter 5 base as opposed to a pw file For information about saving pathways to pw files see Sav ing a Pathway or Reaction to the Database or a File on page 46 Continue to the next sections to add components and reactions to the Graphics window Adding a Component You can add any number of components and connectors in the Graphics window to form any number of reactions in a pathway A set of reactions in the Graphics window represents one pathway You can add components to pathways by e drawing a new component e drawing an existing component e selecting a component from the Database Explorer Drawing a New Component When you draw a new component and name it Vector PathBlazer first searches the database for any components with the same primary name or with the same synonym For example a common synonym of hexokinase is glucokinase If you wanted to create this enzyme in the database by drawing it and you entered the name glucokinase Vector P
47. in Database Explorer 13 objects in Graphics window 18 Status bar hiding 11 Stepwise reaction adding from Graphics window 125 in pathway building 138 Strict search definition 56 Subcellular Location GO annotation 161 Subsets adding components to 130 adding reactions to 130 adding search results 59 60 creating 34 130 creating component subsets from reaction pathway 35 creating intersection of 34 creating reaction subsets from pathway 35 creating union of 34 deleting 35 selecting for pathway building 134 Symmetric layout applying 25 description 25 properties 27 Synonym adding to component 117 annotation field 43 definition 6 drawing a new component 113 System requirements 2 T Tab delimited file for expression values 174 Technical Support 4 Template creating expression 166 creating template from Vector Xpression 176 editinga 170 editing expression 170 importing expression 171 importing expression data with 168 Text View Components folder 29 description 12 28 Pathway folder 28 Reaction folder 29 TransPath auxiliary files 95 custom dictionaries 95 description 93 import instructions 96 source files 93 Trial License 183 Troubleshooting general problems 203 import problems 204 U Unhiding objects in Graphics window 19 Union of subsets 34 Updating database 11 URLs predefined 107 yv Vector Xpression creating template from for expression data import 176 finding components in PathBlazer from 177 interaction
48. in Specifying Path way Direction and Interaction Generality on page 137 For example if pyruvate is specified as the starting component and glycolysis is built in the reverse direction the result is a pathway ending in glucose If glucose is specified as the starting component and a pathway is built in the forward direction the result is a pathway ending in pyruvate Note Ifa synonym is used to identify a component and the synonym is associated with more than one component a list of components associated with the synonym displays Select one component from the list and click OK to continue Identify the end component or pathway by selecting the Build Pathway to Component or the Build Pathway to Pathway checkbox Selecting an end component or pathway is optional Also if you do not select this checkbox then the through component checkbox is unavailable You can either browse for the component or pathway name by clicking the Browse button and selecting a component or pathway from one of the component or pathway subsets in the data base or you can enter the name of the component or pathway in the text field Synonyms can also be entered in the text field Note If you are building a pathway from a small subset it is recommended that an end component is not selected Identify the through component by selecting the Build Pathway through Component checkbox Selecting a through component is optional You can either browse for the component na
49. in the database for which the unique ID is included in the lt substance ID gt element The value of lt substance ID gt is referenced by any reactions in which the component is included Each of the elements between the attribute lt substance gt describe annotations of the component lt list_of_substances gt lt substance ID Phosphopyruvate hydratase DB KEGG Disease Source Description Also acts on 3 phospho D erythronate Ki of phosphonoacetohydroxam ate is 15 picoM as the trianion with saturation Mg ion Biochemistry 1984 23 2 79 Crystal structure of the inhibitor complex Biochemistry 1994 33 6295 6300 gt lt synonyms gt lt name gt 2 Phospho D glucerate hydro lyase lt name gt lt name gt 2 Phosphoglycerate dehydratase lt name gt lt name gt EC 4 2 1 11 lt name gt lt name gt Enolase lt name gt lt name gt Phosphopyruvate hydratase lt name gt lt synonyms gt lt type gt Protein Enzyme EC EC 4 2 1 11 lt type gt lt list_of_origin accesses gt lt origin access Text gt lt database gt AAE lt database gt lt access gt aq_484 eno lt access gt lt origin_access gt Importing Data Chapter 4 lt origin access Text gt lt url gt http www rcsb org pdb cgi explore cgi pdbld 7ENL lt url gt lt origin_access gt lt list_of_origin _ accesses gt lt organisms gt lt organism Class 0 Name Aeropyrum pernix log_op 154137832 gt lt organism Class 0 Name Agrobacteriu
50. of an edge slope Unchecked Off multiplied by a thousand Layout Quality Draft Determines how quickly a layout is Jei regraphed and the final quality of a Table 3 2 Settings for Hierarchical layout 26 Working with Pathways Chapter 3 Incremental Layout Respect Flow Attempts to place new nodes in the current flow Reduce Crossings Attempts to reduce connector cross ings Connectors Routing Orthogonal Routing Turns all connectors to right angles Calculated Sizes Horizontal Spacing Vertical Spacing Undirected Layout Checked On Disregards direction of connectors Unchecked Off Table 3 2 Settings for Hierarchical layout Continued Symmetric Tab The Symmetric layout settings display in Figure 3 24 and are described in Table 3 3 Layout Properties E E Z E Circular Hierarchical 38 Symmetric Spacing Uptions Node Spacing E M Degree Spacing Star Spirals Prevent Node Overlap Cancel Layout Reset Defaults Help Figure 3 24 Settings for Symmetric layout Settings Description Spacing Options Node Spacing Provides a guide A ZE displaying image density Degree Spacing Reduces node crowding for highly connected nodes Star Spirals Checked On Puts nodes adjacent to a highly con Unchecked Off nected node in a spiral Prevent Node Overlap Checked On Prevents nodes from overlapping Unchecked Off Table 3 3 Settings for Symmetric layout 27
51. on page 47 through step 8 on page 50 When you are finished adding annotations click Save In the Save Objects dialog box the opens Figure 3 46 select e the Use the existing objects in the database radio button to use objects that match to the objects in the file by name e the Save objects with new names radio button to create new objects in the database from the objects in the file An incremental number is appended to the newly created ver sion of the object For example if ADP is already in the database then a new component called ADP 2 is created p Component ADP Component ATP Component D Glucose Component D Glucose 6 phosphate Component Hexokinase Select Action Use the existing objects in the database ZI Save objects with new names Cancel Figure 3 46 Options for saving objects that are already present in the database 51 Vector PathBlazer 2 0 User s Manual Opening Crosslinks to External Databases 52 In PathBlazer each component can have two types of crosslinks associated with it database links and or URL links The annotation for describing crosslinks for pathways reactions and components allows you to link directly to corresponding objects in the Vector NTI database if installed or to defined URLs to obtain additional information such as sequences or citations Once crosslinks are assigned as annotations to a particular object either a crosslink s display name or its lit
52. operations in the program includ ing saving and viewing objects In the Properties dialog box most tabs have an Add button Click the Add button and in the dialog box that opens make the appropriate selections values display in the following table Table 3 5 While saving an object when an object is saved by selecting File gt Save As when a path way or reaction is open in the Graphics Window a wizard guides you through adding annota tions by field Figure 3 35 shows the Save dialog box for pathways and reactions The hyperlinks listed in the left pane each correspond to a different type of annotation The available fields in each annotation screen depend on the type of annotation The Next and Back buttons advance the annotation screens in order and the hyperlinks in the left pane jump to the corre sponding screen 37 Vector PathBlazer 2 0 User s Manual 38 Save Pathway _ l E ae Pathway b Save as new pathway Save to Organisms Select a Subset Locations Reference f Database lal All Pathways Cross Links Eile tame do Components d Properties Constants Mame Reaction GOGO rar Conditions f Datasource Organisms Locations Validity Unknown D Cross Links d Pathways Disease Complete 7 3 Description Back Next gt seve Cancel Help A Reaction Gizo pero Screen Navigation Hyperlinks Annotation Screen Navigation Fields Buttons Fig
53. page 157 or they can be applied automatically during the GO annotation import process described on page 159 GO annotations store information about the taxonomy organism and subcellular location of an object Using the feature described in this section you can propagate this information from the GO annotation to the Organism and Subcellular Location annotation fields of PathBlazer objects This propagation is assigned to all objects that already have GO annotations in a subset you select Organism Population lf an object in the PathBlazer database has a GO annotation and it contains information about taxon the GO term for organism PathBlazer adds this organism name to the object s Organism annotation field If before this procedure an object has only a GO annotation after it the Organism field is also populated Subcellular Location Population lf an object in PathBlazer database has a GO anno tation and it contains information about a subcellular location PathBlazer adds this sub cellular name to the object s Subcellular location annotation field Therefore if before this procedure an object has only a GO annotation after it the Subcellular location field is also populated Use the following steps to assign one of these GO Terms to database objects 1 Select Tools gt Manage Gene Ontology gt Populate lt category gt Attribute 161 Vector PathBlazer 2 0 User s Manual 2 Inthe Populate lt category gt Attribute di
54. page 37 The option for GO annotations in the Condition Type drop down menu opens a dialog box unique for working with GO annotations For more information see Search Database by GO Annotation on page 61 55 Vector PathBlazer 2 0 User s Manual The options for Location and Organism in the Condition Type drop down menu have two additional conditions for Search Type Strict Search and Non Strict Search Figure 3 53 Condition Type Organism Search Type GZ Strict Search C Nor Strict Search Add Condition x NOTE Performing a Strict Search will return only objects that contain the requested value annotation for location andor organiem A Non Strict Search will return that same set of objects plus objects that contain no valuevannotation for location andor organism Add Cancel Help Figure 3 53 Extra search type options when searching for Location and Organism These search types described in the panel below the text boxes are based on the defini tions of In Known In and Not In In means that an object is definitively known to be in certain organisms or locations only For example the protein product for the oncogene ERBA is the ERBA receptor and has been definitively located to the nucleus Therefore it is not located anywhere else in the cell In Vector PathBlazer the subcellular value for the component ERBA would be lt Location In Nucleus gt Known In means that an object is definit
55. particular expression data file or pathway and are used to display all expression data on components in Discovery View or reaction nodes in Metabolic View regardless of source data files or associated pathways For exam ple you might be measuring expression changes in a normal versus a disease state Expres sion values for the normal state may be between 0 and 0 5 while the disease state results in a marked upregulation of all genes to a range of 1 to 1 5 You associate the color blue with the 0 to 0 5 range and red with the 1 to 1 5 range When you view the expression data on the pathway components components associated with expression genes are colored blue when expression values for the normal state are displayed and red when expression values for the disease state are displayed To view the color key of the range or expression values in the associated experiment open the Expression Palette by selecting View gt Expression Palette Figure 8 18 The Expression Pal ette is anchored on the right side of the screen by default but can be converted to an indepen dent window by clicking on the double line on the top of the window and dragging and dropping it anywhere on the screen when its borders retract to a smaller rectange To re anchor it on the right side of the screen again drag it to the right and drop it when its borders expand to fill the right side or double click on its title bar to return it to the right side If the palette is tur
56. reversed Protein protein interactions cannot be reversed 2 Select Reverse Reaction from the shortcut menu The Reaction Properties dialog box opens to create a new reaction Figure 3 34 In the Name field the characters b are automatically appended to the name of the reaction to indicate it is a reverse reaction If a formula is entered in the original reaction the Formula field displays the reverse of the orig inal reaction Any other annotations that were associated with the original reaction remain with the reverse reaction Add or modify any annotation including the name and then click OK Reaction Properties E E x Locations Cross Links GO Annotations General Constants Conditions Pathways Organisms Hame Datasource PO Type Generic e Formula CPD 690 GLA FATF AWATEA gt CPD 6917 4 Disease Description Confidence Cancel Help Figure 3 34 Reaction Properties dialog box The reverse reaction is added to the All Reactions subset Adding Pathways Reactions Experiments and Components to the Graphics Window 36 The Database Explorer window interacts with the Graphics window by allowing you to select objects in the List Pane and either drag them or open them so that they are drawn in the Graph ics window The following methods are described in more detail in the context of drawing path ways in Chapter 5 Drawing Pathways but they are briefly listed here
57. system for com patibility with the Vector PathBlazer system requirements and upgrade it as necessary To do this using MS Internet Explorer go to the Downloads page of the Invitrogen InforMax web site http www informaxinc com and follow the instructions This option is not avail able using Netscape Navigator Using Online Help In the Online Help for Vector PathBlazer you will find explanations of the features in Vector PathBlazer as well as tips to guide you through the program s basic functionality In the software there are several ways to open Online Help select Help gt Help Topics from the menu bar In the Online Help that opens you can browse through the Table of Contents or the Index or launch a word search of the Online Help application Press F1 or click the Help button from any open dialog box opening its associated help topic If pressing F1 fails to open an Online Help topic select Help gt Help Topics opening Online Help Proceed with a browse through the Table of Contents or Index or do a word search Your topic may be in the Help files but inadvertently not linked to its associated dialog box Topics may be titled by their function rather than the dialog box name For example the New Molecule dialog box associated topic is named Creating a New Molecule Tips for using Vector PathBlazer online Help Click Help Topics to show or hide the Contents Index and Search tabs Click Print to print the curr
58. type gt lt name gt GTP Ras GDP GEF amp gt Ras GTP GDP lt name gt lt effect gt exchange lt effect gt lt reversible gt false lt reversible gt lt references gt Importing Data Chapter 4 lt reactants gt lt item type Molecule xlink type simple xlink href Mmolecule xml ID MO000000005 xlink show new xlink actuate onRequest gt MOO0Q00000005 lt item gt lt item type Molecule xlink type simple xlink href molecule xml ID MO000000007 xlink show new xlink actuate onRequest gt MO000000007 lt item gt lt reactants gt lt produces gt lt item type Molecule xlink type simple xlink href molecule xml ID MO000000004 xlink show new xlink actuate onRequest gt MO000000004 lt item gt lt item type Molecule xlink type simple xlink href molecule xml ID MO000000006 xlink show new xlink actuate onRequest gt MO000000006 lt item gt lt produces gt lt enzyme gt lt item type Molecule xlink type simple xlink href molecule xml ID MO000000024 xlink show new xlink actuate onRequest gt MO000000024 lt item gt lt enzyme gt lt Reaction gt TransPath Auxillary files gene xml This file contains information about genes Only information not contained in molecule xml is extracted from this file Some additional links are stored as crosslinks to external databases annotate xml This file contains additional annotations about function structure kinetics mechan
59. 010 Glycolysis Gluconeogenesis PATH MAP00071 Fatty acid metabolism GENES HSA 124 ADH1A 125 ADH1B 126 ADH1C 127 ADH4 128 ADH5 130 ADH6 131 ADH7 DISEASE MIM 103700 Alcohol dehydrogenase IA class l alpha polypeptide MOTIF PS PS00059 G H E x 2 G x 5 GA x 2 IVSAC 1 ftp ftp qenome ad jp pub kegg ligand ligand doc 15 Vector PathBlazer 2 0 Users Manual STRUCTURES PDB 1A4U IAI 1A72 1ADB 1ADC 1ADF 1ADG 1AGN 1AXE 1AXG DBLINKS IUBMB Enzyme Nomenclature 1 1 1 1 ExPASy ENZYME nomenclature database 1 1 1 1 Component Annotation Field Name Description in Vector PathBlazer Entry EC Enzyme Commission number Component Class EC Number Also appended to the reaction name Example R00754 EC 1 1 1 1 Name Recommended name and any Component Name alternative names of the enzyme First entry is imported as the primary name and is appended with the E C number This becomes the unique iden tifier in Vector PathBlazer Component Synonym All other entries are imported as syn onyms SysName Systematic name given by the Component Synonym Enzyme Commission which repre sents the nature of the chemical reaction Comment Text information about the enzyme Component Description Genes Link information to KEGG gene cat Component Organism alogs 3 letter organism abbreviation is fol lowed by the list of genes that encode the enzyme For a key to the abbreviations see ftp ftp genome ad jp pub keg
60. 1 9 2 Demo Pathway q pL CASR_HUMAN UserPPI PPI role Trapped protein i 12 1 fall jbh Tao BIND Probable component of se 12 2 Lu Experiments plcb3 BIND putative plasma membran 12 2 4 Lcb4 BIND sphingoid long chain base 12 2 Ad CC2_HUMAN UserPPI PPI role Trapped protein i 12 1 Se Database C Documents SO Settings jill INFORMAXINC My Documents My PathBlazer DatalPathBlazer PathBlazer_ demo ra mdb Figure 3 30 Database Explorer showing components in Details View Original source database displays in the Datasource column Sort a column by clicking on the column header An arrow is placed in the column header to indicate that sorting is based on that column An up arrow designates an ascending sort order and a down arrow designates a descending sort order Resize column widths by dragging the divider between columns to the left or right to reduce or enlarge the column width Remove columns from the display by selecting More from the shortcut menu In the Col umn Settings dialog box a check next to the column name means that it is displayed Figure 3 31 To hide columns from the display uncheck the box next to the column name The Name column cannot be hidden You can also select a column name and click Hide to hide it or Show to display it ES La e Description ll Formula The selected column should be 150 piels wide Figure 3 31 Column settings dialog box for custom
61. 10 default database 6 description 6 opening in PathBlazer Viewer 14 selecting database for use 10 Merge Option dialog box 67 Merging components criteria 68 description 45 during data import 67 manually 45 merge rules during import 68 Merging data results 69 Metabolic View building a pathway 138 description 14 109 opening new Graphics window 112 N Navigating Database Explorer 31 Graphics window 17 Non strict search definition 56 Not In description 56 O Object properties viewing 19 Online Help 3 Ontology See Gene Ontology 153 Opening components in Graphics window 36 118 121 pathways in Graphics window 14 37 reactions in Graphics window 37 125 Organism GO annotation 161 Organizing data 33 Overview window resizing images in Graphics window 17 tiling with Palette window 18 P Palette window commonly used molecules 111 component shapes connector links 110 description 12 hiding 12 moving 12 reanchoring in position 12 Panning in Graphics window 17 PathBlazer interaction with Vector Xpression 166 main features 5 overview 5 tools opened from Vector Xpression 166 PathBlazer Viewer elements 11 launching 10 opening a mdb file 14 opening a pw file 14 Pathway annotation fields 39 browsing in Database Explorer 31 copying 33 default colors 138 definition 7 deleting 33 Discovery View description 14 displaying database crosslinks 52 graphical representation in Vector PathBlazer 14 Metabolic View description 1
62. 20 amp sub mit Submit Bind Reaction Link http bind ca cgi bin dat BIND Interaction Link aget get search amp rec type 4 amp type int amp id s DIP Component http dip doe mbi ucla edu dip DIP DIP Node Link view cgi PK s DIP Reaction Link http dip doe mbi ucla edu dip DIP DIP Interaction Link view cgi IK s Expasy Enzyme Link hhttp www expasy orgd cgi bin get Expasy Enzyme Link enzyme entry 2 7 1 1 Expasy Prosite Link http www expasy org cgi bin get Expasy Prosite Link prosite entry PS00378 Genpept Link http ncbi nim nih gov entrez query fcgi cmd Retrieve amp db pro tein amp dopt Gen Pept amp list_uids 83035 IUBMB ttp www chem qmul ac uk iubmb Enzyme Commission enzyme EC d html KEGG Compound ttp www genome ad jp dbget bin KEGG Component Link www_bget compound C00022 KEGG Enzyme ttp www genome ad jp dbget bin KEGG Enzyme Link www_bget enzyme s KEGG Reaction Link http www genome ad jp dbget bin KEGG Reaction Link www_bget rn s OMIM link http Awww ncbi nim nih gov htbin OMIM Disease Link post Omim dispmim 138079 PDB http www rcsb org pdb cqi PDB Structure Link explore cgi pdbld 1BDG PIR Sequence http pir georgetown edu cgi bin PIR Protein Link nbrfget xref 1 amp id JT0482 PROMISE http metallo scripps edu PROM Protein Active Sites ISE s html Table 4 7 Pre defined URLs Genpept Protein Link 107 Vector PathBlazer 2 0 Use
63. 4 opening in Graphics window 14 renaming 33 saving from file to database 51 viewing in Text View 28 viewing properties 28 Pathway building adding stepwise reactions 138 assembly parameters 134 examples 139 excluding components 136 from Database Explorer 139 hiding components 136 in Discovery View 138 in Metabolic View 138 selecting reaction subset 134 135 setting additional step number 136 setting interaction generality 137 setting maximum step number 136 specifying direction 137 specifying start end through component 135 turning pooling off 136 Pathway Viewing Area elements 12 Master Text Views 12 Pooling definition 136 turning off for pathway building 136 Populating GO Organism annotation 161 Populating GO Subcellular Location annotation 161 PPI data display 102 description 100 import instructions 100 Pre loaded data crosslinks to Vector Advance 52 description 7 in gene expression display 175 Printing images text from Graphics window 63 Properties Component Class tab 43 Component tab 39 Condition tab 44 Constants tab 44 Cross Links tab 41 Expression Data tab 44 General tab 39 GO Annotations tab 43 graphical 19 graphical layout 25 in Database Explorer 31 in Text View 29 Locations tab 42 object 19 Organisms tab 40 Pathway tab 44 References tab 43 Synonyms tab 43 viewing annotations 37 Proprietary data defining components 102 defining components in import 102 defining pathway
64. 52 CHAPTER GENE ONTOLOGIES This chapter describes gene ontologies their import and assignment to PathBlazer compo nents reactions and pathways Topics in this chapter include Introduction to Gene Ontologies on this page Importing Gene Ontology Terms on page 154 Searching Gene Ontology Terms on page 156 Manual Annotation of PathBlazer Objects with GO Terms on page 157 Importing Gene Ontology Annotations on page 159 Population of Organism Subcellular Location Attributes Based on GO Annotations on page 161 Introduction to Gene Ontologies Gene ontology GO is a fixed vocabulary of biological terms that also includes their biological classification s Because they are standarized when gene ontologies are assigned to biological objects there are no ambiguities in their definitions and classifications The Gene Ontology consortium provides two types of information on their website http www geneontology org 1 the Gene Ontology itself a fixed vocabulary dictionary of terms and their place in classification called GO terms file in this chapter and 2 Gene Ontology annota tions a file of specific GO terms that are already linked to real life or common biological notions such as gene names biological processes cell components etc called GO Annota tions file in this chapter For example the common biological term apoptosis corresponds to gene ontology term GO 0006915 This chapter is divided loose
65. 6N5013P3 Glucose Aldolase Figure 3 27 Components folder in the Text View tab The Text View tab contains no Experiments folders Creating Alternate Graphical Views When you first open or create a pathway in the Graphics window only the Master View and the Text View tabs display You might build your pathway in the Master View and then decide that you want to use several different graphical versions of the pathway for different publication or teaching purposes Vector PathBlazer allows you to create Alternate Views for these kinds of purposes that are stored within one pathway An Alternate View can either be an exact copy of an existing view or a new view When you copy an existing view all of the graphical properties of that view are copied When you create a new view the default graphical properties of the Master View display In an Alternate View you cannot add components connectors or reactions to the pathway You can however modify the graphical properties of the pathway elements and the graph itself change the layout properties hide pathway elements and overlay gene expression 29 Vector PathBlazer 2 0 User s Manual data sets on the pathway Furthermore if a component is added to a Master View after Alternate Views are created the new component is broadcast or added to the Alternate Views When you save the pathway and reopen it later the Alternate Views are saved with the pathway and include the modificati
66. Based on the selected parameters the program assembles a pathway that consists of the steps in glycolysis The pathway displays in the Graphics window and is initially enlarged so you can easily view the components Figure 6 5 Use the buttons in the toolbar and the commands in the View menu to resize the image The starting component is shaded green and the ending component is shaded red Figure 6 6 The title bar indicates that the pathway is automatically generated and when you save the path way the name Automatically generated is entered as the default in the Name field Automatically Assembling Pathways Chapter 6 ES Automatically generated pathway 4 Discovery unrestricted view Database Glyceraldehyde 3 phosphate mene 4 Master View Figure 6 5 Glycolysis automatically assembled with starting component shaded royal blue font modified to white for image ES Automatically generated pathway 4 Discovery unrestricted view Database ATP PyK ATP H20 4 gt Master View E Figure 6 6 Ending component is shaded red Building a Pathway from a Starting Pathway to an Ending Component Description This example describes how to assemble a pathway by entering a from pathway and a to component 143 Vector PathBlazer 2 0 User s Manual Input Output Steps Assembled 144 Pathway The starting object is the pathway created and saved in the first example Building a Pat
67. C Organisms Name Species name cont d Values Arabidopsis thaliana Takifugu rubripes Bos taurus Dictyostelium discoi Caenorhabditis ele deum gans Neurospora crassa Homo sapiens Xenopus laevis Rattus norvegicus Drosophila melano Saccharomyces cere gaster visiae Zea mays Mus musculus Escherichia coli Schizosaccharomy Plasmodium falci ces pombe parum Danio rerio Oryza sativa Cross Links Display Name Name that displays on the shortcut menu in the Graphics window for a selected object If no name is entered the Accession ID or the URL displays See fields for Accession ID and URL below String Type Specifies a link from an object in the Vector PathBlazer database to either the Vector NTI database or to a URL Values Database URL Database Opens object with the corresponding object Type name in the Vector NTI Suite or Advance data Database base if installed See also description of Accession ID field Values Component VNTI DNA RNA VNTI PROTEIN VNTI CITATION VNTI BLAST Pathway and Reaction VNTI CITATION Accession ID Unique object name in the VNTI Suite Advance Type database Only names of DNA RNA and pro Database tein molecules citations and Blast results can be linked from Vector PathBlazer to the VNTI database Example GALA YEAST String Table 3 5 Annotation fields and values for pathways components and reactions Continued 41 Vector PathBlazer 2 0 User s Manual
68. CTION LIST REACTION LIST REACTION LIST REACTION LIST SPECIES P122 PWY Fermentation heterofermentative lactate fermentation ALCOHOL DEHYDROG RXN ACETALD DEHYDROG RXN ACETALD DEHYDROG RXN PHOSACETYLTRANS RXN PHOSACETYLTRANS RXN PHOSPHOKETOLASE RXN DLACTDEHYDROGNAD RXN PEPDEPHOS RXN PEPDEPHOS RXN 2PGADEHYDRAT RXN 2PGADEHYDRAT RXN 3PGAREARR RXN 3PGAREARR RXN PHOSGLYPHOS RXN PHOSGLYPHOS RXN GAPOXNPHOSPHN RXN PHOSGLYPHOS RXN 1 2 1 13 RXN GAPOXNPHOSPHN RXN PHOSPHOKETOLASE RXN 1 2 1 13 RXN PHOSPHOKETOLASE RXN PHOSPHOKETOLASE RXN RIBULP3EPIM RXN RIBULP3EPIM RXN 6PGLUCONDEHYDROG RXN 6PGLUCONDEHYDROG RXN R84 RXN R84 RXN R81 RXN ALCOHOL DEHYDROG RXN ACETALD DEHYDROG RXN PHOSACETYLTRANS RXN DLACTDEHYDROGNAD RXN PEPDEPHOS RXN 2PGADEHYDRAT RXN 3PGAREARR RXN PHOSGLYPHOS RXN 1 2 1 13 RXN GAPOXNPHOSPHN RXN PHOSPHOKETOLASE RXN RIBULP3EPIM RXN 6PGLUCONDEHYDROG RXN R84 RXN R81 RXN HPY 91 Vector PathBlazer 2 0 User s Manual The pathway is stored under name heterofermentative lactate fermentation and is assembled from the highlighted reactions Instructions for Importing BioCyc Data You must have downloaded the data files described in BioCyc Source Files on page 86 to your local file system The databases from BioCyc collection can be imported separately or as a group You can import data either into the default PathBlazer database or into a new separate database you create before the dat
69. Condition Name Condition that can be associated with reactions Values pH range Temperature range Value Value of the condition Number Pathway Pathway Name Pathways that are associated with reactions String Expression Expression data Reference to original database if available Data base file Table 3 5 Annotation fields and values for pathways components and reactions Continued Annotation Fields for Connectors The annotations for describing connectors are more limited than those for pathways reactions and components and are all contained in one dialog box Figure 3 38 Change the annotations of a connector by selecting it in the Graphics window and then selecting Connector Properties from the shortcut menu to open the Connector Properties box Connector Properties ETZ Zi EA Figure 3 38 Connector Properties dialog box 44 Working with Pathways Chapter 3 Table 3 6 lists the annotation fields and values for connectors Field Description Direction Designates the direction of the connector Values Not Specified Input Output Input Output Designates the role of the connector Only valid if Direction Input Values Not Specified Normal Activating Inhibiting Stoichiometric Constant Quantity of a component participating in the reaction Number Transition Probability Can be used to describe the probability of a change of state Number Table 3 6 Annotation fields and values for connectors
70. Expression Run or experiment that is associated with the gene in that row The column header can be any text string and will appear as the time point disease state etc identi fier in Vector PathBlazer for the values in that column Once a set of mappings is established a template file can be defined from the links between a set of gene names from the gene expression file and a set of component names in Vector Path Blazer An example expression data file is shown in the following figure Figure 8 14 The first column of the file contains a list of gene names that correspond to the enzymes in glycolysis This file is included with the Vector PathBlazer installation It is located in a directory separate from the default database the directory differs depending on your operating system In Windows 2000 for example it loads in the following directory C Documents and Settings MyDocuments My PathBlazer Data DeRisi_glycolysis_ TCA Expression Data txt The other columns contain expression ratios for six time points that is six Expression Runs The labels displaying the time points 9 hours through 21 hours will display as the titles of the Expression Runs in Vector Path Blazer 9 hours 11 5 hours 13 hours 15 hours 16 5 hours 16 5 hours 21 hours CD19 0 046799 O 10046011 003524172 0 2707404 0 2936917 0 6397514 1 795159 FGI O 254935562 06992296 0 67479251 0 560647922 0 57035708 UL IIEI TGAO 0 014967 GLH 0 499527 O 1108275 069267464
71. Figure 4 8 PathBlazer Import EE x Create and store reverse reactions for reactions of known directionality edi Foot folder C Documents and Settings jil NFORMAXINC Browse GE i Reaction main freaction_mainlst Browse er Reaction list zeda Browse KN Reaction data reaction Browse KO Compound file rrari Browse 4 a Enzyme file enzyme Browse deda genome Browse Default Back Hent gt Cancel Help Figure 4 8 KEGG files selected for import Continue to select the data file for import by clicking the Browse button adjacent to each field locating the corresponding file in the Browse for File dialog box and clicking Open The complete path to the file displays in each field e Optional Select the Create and store reverse reactions checkbox If this box is selected it creates reverse reactions for reactions with a KNOWN directionality e Optional Select the Save intermediate XML file checkbox to save the XML file that is created from the KEGG source files Specify a location and a file name for the XML file by clicking the Browse button adjacent to the field Select path for intermediate XML file When you are finished selecting the KEGG directory and files click Next In the Merge Option dialog box select the options appropriate for merging the data See Merge Option Dialog Box on page 6 7 for more information To import the data click Next The data l
72. GOE 297451711 SDH3 0 35254499 0 13607054 0 51412523 0 96216935 135976768 2 17717409 A 96230364 Figure 8 14 Example of expression data file that can be read by Vector PathBlazer 1 genomic scale Science 278 5338 680 6 DeRisi JL Iyer VR Brown PO 1997 Exploring the metabolic and genetic control of gene expression on a 175 Vector PathBlazer 2 0 User s Manual Exchanging Data Between Vector PathBlazer and Vector Xpression Creating a Template from Vector Xpression 3 1 While directions in this chapter cover creating a expression template from PathBlazer Creating an Template Automatically on page 166 you can also create a template starting from Vector Xpression 3 1 To do so complete the following steps 1 In the Vector Xpression Database Explorer select Expression Genes from the Tables drop down list and then select the gene s that you want to map or Open an Expression Runs Viewer Runs Project Viewer or Experiment Viewer displaying data with genes that you want to map Select the gene s that you want to map 2 Inthe open viewer select Tools gt Create Template in PathBlazer 3 This opens the Create Template Wizard Click the Browse button to locate and select the PathBlazer database in which you want to create the mapping template Click Next 4 The Create Template Wizard is a PathBlazer feature At this point continue configuring the template beginning with step 5 on page 167
73. Ignore Paths through these Components bi Small Molecules a le Dont Pool Components in Subset bi Small Molecules E I Hide these Components A Choose Component Subset ae Reactions OEM All Reactions all glycolysis I Show only connecting components Calculate critical points Connection Length Pathway Direction Mas Number of Steps Extra Steps Direction Interaction Generality fi 0 E fo E Forward Unlimited Figure 6 9 Building a pathway through a selected component 12 Click OK to start assembling the pathway Assembled The starting component is royal blue with font changed to white for this image and the Pathway through component is shaded light green Figure 6 10 ES Automatically generated pathway 5 A Discovery unrestricted view Database d d iol x ae 4 phosphate See 7 Ee Tre 5 phosphate 2 N Dihydroxyacetone phosphate o D EO gi dd as da Hid Hd ei ADP 4 A Master View A Figure 6 10 Glycoloysis pathway through Fructose 6 phosphate automatically assembled the through com ponent Fructose 6 phosphate is circled 146 Automatically Assembling Pathways Chapter 6 Adding a Stepwise Reaction Description This example describes how you can add one or more reactions that you specify to an assem bled pathway Input Output Steps Starting component is Glucose number of pathway steps is three Reaction 1 Glucose ATP hexok
74. Internet connectivity To get key contact Tech Support with License and Hardware ID pa Figure A 4 Static License dialog box 185 Vector PathBlazer 2 0 User s Manual 186 Note Notes Enter your name organization phone number and email address in the appropriate fields This sets the user information in Vector PathBlazer If you already entered your personal information on the Personal tab it should appear here when you open this dialog box In the License field enter your Vector PathBlazer static license number provided in the letter accompanying your CD ROM and or manual Click the Apply button Your software is registered immediately If the registration fails because of a missing connection to the Invitrogen licensing server an appropriate message immediately displays In such a case you can contact Invitrogen InforMax Technical Support or Sales see and provide them your computer s hardware ID and your license number They Once you receive the registration key enter the key in the Key text box of the Static License dia log box Make sure the License Number is entered appropriately and click Apply If the Key matches your license number and computer hardware ID the license is registered No connec tion to the Internet is required in this case e Once you have applied your static license notice that the Applications tab reflects your static license status e If you want to reset your static lice
75. MasterView Figure 5 15 Drawing a new component Adding An Existing Component from the Database Explorer You can drag and drop any component that is already present in the database directly from the Database Explorer onto the Graphics window to add the component to a reaction or pathway For example you might have drawn the components that are involved in the glycolysis pathway de novo and saved them to the database and then you want to reuse some of these compo nents to draw the gluconeogeneis pathway 1 To add a component this way locate the component you want to add to the reaction or path way in a subset of the Components folder in the Database Explorer Select it and drag it into the Graphics window The component is added to the Graphics win dow in the location where you dropped it and its name displays Figure 5 16 If a compo nent has a type associated with it such as Enzyme then the appropriate graphical properties associated with it display such as an oval 121 Vector PathBlazer 2 0 User s Manual 122 3 Add as many components to a single Graphics window as required EES vector PathBlazer 2 New PathWay 1 ae f la x File Edit View Tools Layout Window Help gt ed EE j E d OA I Expression Data Sets None Expression Runs IR GS J JB Z UJA R SS x ZN New PathWay 1 Discovery unrestricted view Database 7 ZBE GO Glucose Undefined v
76. NA synthetase glyQ glyS GUO GLYS 2 GLYQ MONO MER 2 GLYS MONOMER The component will be named glycine tRNA synthetase The gene names of proteins forming this complex glyQ and glyS will be stored as crosslinks to EcoCyc genes information and in the component description Subunits GLYQ and GLYS will be crosslinked to protein information and stored in the description as well File proteins dat This file contains information about proteins polypeptides which do not have EC classification Components classified as proteins are created in the PathBlazer database Importing Data Chapter 4 The following is an entry from the proteins dat file Parts which are extracted by PathBlazer are shown in bold If MODIFIED FORM or UNMODIFIED FORM is present the modification unmodification reaction RED THIOREDOXIN MONOMER gt OX THIOREDOXIN MONOMER is created and stored as a separate reaction object UNIQUE ID RED THIOREDOXIN MONOMER TYPES red thioredoxin COMMON thioredoxin 1 NAME COMMENT enzyme Biosynthesis of cofactors carriers Thioredoxin glutare doxin glutathione GENE TRXA LOCATIONS INNER MEMBRANE MODIFIED OX THIOREDOXIN MONOMER FORM SPECIES E coli SYNONYM reduced thioredoxin SYNONYM TrxA SYNONYM thioredoxin SH lt SUB gt 2 lt SUB gt File transporters col This file contains information about transporters The file is in tabular format An entry Z3799 MONOMER putative ATP synthase beta subunit H cytoplasm H2O
77. Properties from the shortcut menu The Object Properties box opens Figure 3 14 Object properties refer to the node properties or display properties of an object in the Graphics window including the object s name its font characteristics and its shape characteristics Note that the drop down list at the top of the win 19 Vector PathBlazer 2 0 User s Manual 20 dow displays Selected Node Properties This drop down list toggles to Selected Graph Prop erties which are described below Object Properties j 3 Selected Node Properties D Background Color Border Color Border Width Fit To Name Ellipse Figure 3 14 Object Properties box for a component It is not possible to change an object name in the Object Properties dialog box The rules for naming an object are listed in Drawing a New Component on page 113 Change the Font Background Color or Border Color by selecting the field and click ing the Browse button on the right side of the row A dialog box for selecting either font characteristics or colors displays Select the settings you want and click OK Change the Border Width Fit To Name and Shape by selecting the options from the drop down list for each The Fit To Name field refers to how the object is shaped when it is resized Values are No fit can resize in any direction Example gt Tight fit cannot resize If object has been resized the size reverts to the original default size
78. Reaction Figure 6 14 Adding a stepwise reaction from a component in an automatically assembled pathway 148 Note Automatically Assembling Pathways Chapter 6 In Figure 6 14 the components ADP and ATP are pooled that is instead of redisplaying these components again in the added reaction the existing components used in the first reaction are reused in the fourth reaction Building A Link Between Two Pathways Description This example describes how to establish a link between two existing pathways Input The starting pathway is the glycolysis pathway you built and saved in the first example Building Steps a Pathway from a Starting Component on page 139 The target pathway for the link is the TNFR Signaling Pathway in the PathBlazer database 1 Select Tools gt Build a Pathway gt Build Discovery Pathway 2 In the Build a Pathway dialog box select the Build Pathway from Pathway checkbox Click the Browse button and locate the pathway Pathway glycolysis 2 Steps or by the name you assigned the pathway when you created it 3 Select the second Build Pathway to Pathway checkbox Click the Browse button and locate the pathway TNFR Signaling Pathway in the Signal Transduction Pathways sub set In the Include Reactions from Subset field select the All Reactions subset Set Max number of steps to 10 Set Extra steps to 0 select Ignore Paths through these Components and select the Small Molecules subset oo pa pi
79. Vector PathBlazer 2 0 User s Manual 3 Invitrogen life technologies Vector PathBlazer 2 0 User s Manual Published by Invitrogen 7305 Executive Way Frederick MD 21704 www informaxinc com Copyright 2004 Invitrogen All rights reserved This book contains proprietary information of Invitrogen No part of this document including design cover design and icons may be reproduced or transmitted in any form by any means electronic photocopying recording or otherwise without prior written agreement from Invitrogen The software described in this document is furnished under a license agreement Invitrogen and its licensors retain all ownership rights to the software programs offered by Invitrogen and related documentation Use of the software and related documentation is governed by the license agreement accompanying the software and applicable copyright law Vector PathBlazer is a registered trademark of Invitrogen in the United States and other countries Logos of Invitrogen are also trademarks registered in the United States and may be registered in other countries Other product and brand names are trademarks of their respective owners Printed in the United States of America Invitrogen reserves the right to make changes without notice both to this publication and to the product it describes Information concerning products not manufactured or distributed by Invitrogen is provided without warranty or representation
80. You can view the GO terms or search for specific terms assign GO annotations manually to PathBlazer objects as well as update the gene ontologies at a later point All of these topics are covered in the following sections Viewing Gene Ontology Terms To view gene ontology terms in PathBlazer select Tools gt Manage Gene Ontologies gt View Gene Ontology Categories Gene Ontology Hierarchy Browser GEO molecular function GU 00036 4 SEO biological process G0 00087 50 41 behavior G0 0007610 I biological process unknown 00 0 SATU cellular process GU 000998 cell communication 00 0007 cell death G0 000871 9 cell differentiation 4 U0 00301 5 cell growth andor maintenance cell motility G 0 0006928 AT cell migration G0 0016477 Ld cillarys flagellar motility GU AL muscle contraction 40 00 g H ANE deie Close Help Figure 7 2 Gene Ontology Browser 155 Vector PathBlazer 2 0 User s Manual The Gene Ontology Browser dialog box that opens displays the hierarchical relationships between the gene ontology terms Figure 7 2 The right panel of the dialog box allows you to browse the Gene Ontology tree displayed in the right panel The left panel is used for retrieving gene ontology terms in a search searching Gene Ontology Terms 156 If you do not know a Gene Ontology term you can use search capabilities of the GO viewer select Tools gt Manage Gene Ontologies gt View Gene Ontolo
81. a Static License Testing the License Server Connection Dynamic and Trial Licenses In both the Dynamic License and Trial License dialog boxes press the Test Connection button to review the status of your connection This opens the Server Connection Tester dialog box Figure A 7 ZZ Dynamic Licenses server connection tester EE d x License Server UAL Ask vour administrator for detaile Connection diagnostics http trial informasine com yntitrial yntitral cgi Connection DK Use DLS authorization if applicable YectorNT Trial License Server version 1 2 Apr 7 2003 No licenses available Connection OF User name losh Brown Ge b Internet Connection Settings Connect Clear Figure A 7 Dynamic License Server Connection Tester dialog box The status of the connection displays in the right hand panel For a trial license it will report that there are no licenses available until you request a trial license see Trial License Dialog Box above If the server requires a password it must be entered into the corresponding text box in this dialog box If you want to alter your proxy settings press the Internet Connection Settings button see next section Once the settings are reconfigured press the Connect button to test the connection using the new settings Internet Connection Settings Dynamic and Trial Licenses For Dynamic or Trial licenses press the Internet Connection Settings button in the Dy
82. a import To create a database see Creating a New Data base on page 10 Use the following steps to import BioCyc data into the Vector PathBlazer database 1 Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 2 From an open PathBlazer window select File gt Import 3 In the PathBlazer Import dialog box the first screen of the Import Wizard select Import BioCyc Data The Description box reflects the type of data chosen for import Click Next PathBlazer Import E EA Select import module Import Biol Formated data User PPI Import User PPI data DIP Import DIF data pA Import KEGG v 26 data Trans Innar Trenak data xl Description K data from Biolyc database lt Back Cancel Help Figure 4 11 BioCyc file selected for import 4 In Screen 2 of the Import Wizard enter the name of the organism whose genes you are going to import Figure 4 77 Important This organism will be applied to all entries from this database with the quantifier KNOWN IN unless specific information in a specific entry contradicts it For example if you import the AgroCyc database you might want to enter Agrobacterium tumifaciens This organism name will be applied to all entries taken from the AgroCyc database The organism field can be left empty if for example you import the entire BioCyc database or if for some reason you do not want to specify an organism
83. a reaction subset for reactions including Fructose 6 phosphate In the Graphics window right click on Fructose 6 phosphate and select Add reaction from the shortcut menu In the Add reaction dialog box in the drop down menu select 147 Vector PathBlazer 2 0 User s Manual Input and select the reaction subset containing the glycolysis reaction entries Figure 6 12 Click Search Add Reaction E E Specity the role the component will play in the reactions Hit the search button to find the matching reactions in the database rea Figure 6 12 Add reaction dialog box 13 The Add reaction dialog box displays all reactions in this example there are four in the selected subset that includes Fructose 6 Phosphate Figure 6 13 Select the reaction s and click OK to add the reactions to the selected component x Matching Reactions Reaction Formula glycolysis_rxn4 Fructose 6 phosphate AT _ gluco_rxn2 L pentose_rxn8 pentose_rxn3 Show Reactions with Generality 5 otless Cancel Help Figure 6 13 Selecting reactions to add to the assembled pathway Assembled Once the reaction is added the assembled pathway includes the fourth reaction of glycolysis Pathway Figure 6 14 e E Automatically generated pathway 6 Discovery unrestricted view Database be AE Glucose 6 phosphate isomerase gt a ham Fructose 1 6 bisphosphate Added
84. about the connector to which the component is associated in the reaction Working with Pathways Chapter 3 d Pathway Name Direct Role Stoic Trans Save Reaction Components Reaction 1 of 1 Organisme 1 3 Bisphophogly Input Normal 1 1 000 Glceraldehyde 3 Output Normal 1 1 000 Locations NADH Input Normal 1 1 000 Feference NADA Output Normal 1 1 000 Glceraldehyde 3 Input NotS 1 1 000 Cross Links d Reaction guro rri do Components A Properties Constants Conditions Organisms Locations Cross Links d Pathways Complete Properties lt Back Next gt seve Cancel Help Figure 3 42 Components screen in the Save dialog box that lists all components in a reaction To view the properties of any connector in a reaction select the component and click Prop erties The Reaction Component dialog box lists the properties of a particular connector in a reaction and the component to which it is connected Figure 3 43 To change the compo nent click the Browse button and create a new component or select one from the database To change any of the properties of the connector change the values in the remaining fields Click OK Click Next to move to the next screen or click one of the hyper links to jump to a screen Figure 3 43 Reaction components dialog box The Properties screen for the reaction displays This screen is similar to the first sc
85. action I st file Reactions are then linked to components by matching a component ID from the chemical formulas field in the reaction I st file to the corresponding val 77 Vector PathBlazer 2 0 User s Manual ues in the entry field of the Compound file For example the chemical formula in reaction ROO702 is 2 C00448 lt gt C00013 C03428 CO0080 C00448 matches the corresponding record in the Compound file ENTRY C00448 NAME trans trans Farnesyl diphosphate Farnesyl diphosphate Farnesyl pyrophosphate 2 trans 6 trans Farnesyl diphosphate Thus reaction R00702 is linked to component C00448 which is trans trans Farnesyl diphos phate by primary name in the Vector PathBlazer database Other components in this reaction will be linked C00013 to Pyrophosphate C03428 to Presqualene diphosphate and C00080 to H Component C00448 in this will have stoichiometric coefficient 2 Reaction_main lst File This file is used to determine directionality of reactions For example R00093 C00025 lt C00064 C00026 R00094 C00051 lt gt C00127 R00093 will be directed from right to left If during import the checkbox Create and store reverse reactions for reactions of known directionality is checked the reverse reaction ROO0093 Reverse C00064 C00026 gt C00025 will also be created For R00094 direct and reverse reactions will be created by default Reaction file This file is used to assign a Name and Formula to the reacti
86. again or drag it from its title bar and drop it anywhere when its width returns to a square e Select View gt Zoom and select one of the following submenus Select Fit in window or click the GO icon on the Graphics toolbar to best fit all of the pathway elements in the Graphics window Select a value to zoom to a specified percentage for example 400 Select Zoom in or Zoom out to zoom in or out You can also press the or keys to zoom in and out Select Marquee Zoom or click the icon on the Graphics toolbar to change the cursor to a magnifying glass with a crosshair Drag a wire frame around an area of interest The area is enlarged when you release the mouse Select Interactive Zoom or click the EO icon on the Graphics toolbar to change the cursor to a magnifying glass with a two headed arrow Drag the mouse vertically and horizontally to zoom in and zoom out on the image Jump from connector to the next element component or reaction node by selecting the Navigate connectors button or select Tools gt Navigate Connectors The cursor changes to a compass with an arrow pointing out of it fe When you point with this icon to a connector the view jumps to the next component or reaction node This navigation method is especially useful if you have zoomed in closely on a pathway and want to follow the connectors from component to component Multiple select components reactions and connector
87. age 97 Importing Proprietary Data on page 102 Pre Defined URLs on page 107 For information about importing gene ontologies see ntroduction to Gene Ontologies on page 153 For information about importing expression data see mporting Expression Data with a Tem plate on page 168 Introduction to Importing Data One of the strengths of Vector PathBlazer is that it allows importing data from public and propri etary sources thereby integrating data from different data sources Public data from the KEGG BIND BioCyc TransPath and DIP databases can be imported into Vector PathBlazer as well as user PPI and proprietary data The general workflow that applies to importing public and proprietary data into Vector Path Blazer is 1 Public source files are downloaded to the local file system or proprietary files are formatted as XML files according to the Vector PathBlazer Document Type Description DTD 65 Vector PathBlazer 2 0 User s Manual 2 Source files and other parameters are specified The program converts public data to XML format and the entries in the source files are imported to create pathway reaction and component objects in the database For propri etary data which is already in XML format the program imports the entries in the source files to create objects in the database About Vector PathBlazer Data Import Before you can commence importing data into PathBlazer you must download the data and store it lo
88. aia aztea EEE 5 Maa Bla 5 Vector Path Blazer gia 6 ABERERIK biu AAA 6 PESO AG COD AVA AAO 7 ESE ataa 8 Integration with Vector ADTSSSIOnA ls 8 Chapter 3 Working with Pathways cccccseessseeeeseeeeeeeceeeeneeenseneseeesenseesenesenssneeeesones 9 IES letza ba GA BE dA Aaa 10 Creating a New B Bela 10 Baek ie Up Te e le 11 Flements of Path Blazer Viewer AE 11 Pathway Vile Wile TATT EEE 12 Database Explor AAE 12 Went Barand abera ei ea 13 Working with Pathways in the Graphics Window rruna 13 Openinea PALIN WAY aaa aei 14 Neu Pathways Git aida AA 14 Navigating Objects in the Graphics Window ss 17 Vector PathBlazer User s Manual Customizing Graphical baguea era 19 Viewing Pathways in Text Format AAA 28 Creatine Alternate Graphical eizu 29 Working with Pathways in the Database Explorer rrura 31 Browsmo Pathway NE as a E a aan dae aie eas alae 31 Naming Copying and Deleting ODJECIS AAA 33 BUS EAK Pathway BSE 33 REVersine the Direccion Sa Be aala AAA 35 Adding Pathways Reactions Experiments and Components to the Graphics Window 36 Annotating Pathways Components Experiments Reactions and Connectors 37 Annotation Fields for Components Reactions and Pathways sa 39 Annotation Pichds Tor Connectors AAA 44 Met me Components ABREU 45 Saving PathBlazer Components Reactions and Pathways sara 46 Saving a Pathway or Reaction to the Database or a File ss 46 Saving Reactions Not Going Through a Pathway rss 50 S
89. aling components TransPath focuses on signaling cascades that aim at transcription factors and thus alter the gene expression profile of a given cell helping to bridge the gap between extra cellular signal molecules such as hor mones cytokines etc and the genes responding to these triggers A complete description of the contents of TransPath as well as licensing information is available at http www biobase de pages products transpath html Reference and marketing information is also available in Appendix C TransPath Source Files Upon downloading the TransPath database save the source files in the same folder Two files molecule xml and reaction xml are essential for import Files gene xml annotate xml loca 1 http transpath gbf de 93 Vector PathBlazer 2 0 User s Manual 94 tion xml reference xml and hyperlinks xml are non essential for PathBlazer import They con tain some auxiliary information TransPath starts from the parsing of molecule xml which contains information about molecules They are stored as components in the PathBlazer database During the import of reactions xml these components are connected into reactions Some additional reaction annotations are also extracted from this file File molecule xml This file contains information about components Each component has a unique id specified by lt Molecule id gt tag The name of a component is defined by lt name gt tag and synonyms by
90. alog box that opens select Object type in the drop down menu Figure 7 10 Check the checkbox for one or more subsets whose objects will be assigned the annotation Subcellular locati Populate Organism Attribute Choose Subsets bez x Object type Components r Subsets Components OE GI All Components i Si Small Molecules gpg Demo Components Attribute Type fln T Fopulate Cancel Figure 7 10 Populate lt category gt Attribute dialog box 3 Inthe Attribute Type drop down menu select one of the following logical qualifiers e In Definitively Known to be in one or more organisms If an object is in one or more organisms all others are excluded e Known in Known to be in an organism but all others cannot be ruled out e Not in Opposite of Known in Known not to be in an organism but all others cannot be ruled out 4 Click Populate This applies the specified annotations to all objects that already have GO annotations in the subset s The newly assigned GO annotations will now appear on the GO Annotations tab in the Proper ties dialog box for the objects in the selected subset s Sample Workflow Using Gene Annotations The following example describes a simple workflow using the gene ontology features described in this chapter Use the default PathBlazer demo db that loads with your PathBlazer 2 0 installa tion 1 Download the Gene Ontology Terms file as described in mporting Gene Ont
91. ame Description and Formula for Components and Reactions only display in the Contents Pane Figure 3 30 Each object s name is listed in the Name col umn If a description or formula has been entered text also displays in these columns 31 Vector PathBlazer 2 0 User s Manual b ector PathBlazer 2 E Pie x File Edit View Tools Layout Window Help BE gt gt gt bel EB n GO de S d Expression Data Sets n lone Expression Runs E Sb yr ula 8 aw amp jie sal x calle SIE ZKE ZA PathBlazer Database C Name S Dattasource Description Formula Creaa E Components dpL C64601 UserPPI PPI role Trapped protein i 12 1 fal All Components yay 64613 UserPPI PPI role Trapped protein i 12 1 igi CL molecules fp L C64618 UserPPI PPI role Trapped protein i 12 1 E edeak pL C64641 UserPPI PPI role Trapped protein i 12 1 d TE TE dgn UserPPI PPI role Trapped protein i 12 1 fll intersection jbt SI new bh 4b L Ca channel active DIO EE E Smal Molecules 4bL Ca channel inactive INMY 12 2 Gi test 4b L CACM_YEAST UserPPI PPI role Trapped protein i 12 1 J union jbh 4b L CAP_YEAST UserPPI PPI role Trapped protein i 12 1 ZIO Reactions 4 L carnitine Mol weight 161 2 SMILE C HISNO3 UI 3 Pathways 4 l carnitine dehydratase Catalyzes L carnitinyl Co 17912 Gi All Pathways pL CARNITINYL COA
92. ames nevw enzyme in current file Look for component new enzyme in main Database PREETI Look for components with similar names new enzyme in the main Database PPE eee n a Create new component new enzyme Cancel Figure 5 3 Prompt to search the database for a component The first three radio buttons allow you to search the database for an existing object s More information about those options are provided in the next section To create a new object select the Create a new component radio button Click OK This opens the Component wizard 3 The Component wizard contains a list of screens that allow you to name and add annota tions to a component when you are creating it e f you do not want to add annotations simply name the component in the third screen Continue to step through the wizard using the Next button in each screen until the Fin ish button displays Click Finish to create the component Once the component is saved to the database you can annotate it at any time For a description of each annotation field and its values see Annotating Pathways Compo nents Experiments Reactions and Connectors on page 37 e To add annotations in the first screen of the Component wizard select the Create new component radio button and click Next Figure 5 4 Component a E Ea Use this wizard to either select an existing component from the database or to create 3 new ore ZG Create new co
93. ample C1 and C2 and C3 Click the Custom button for grouping search criteria Parentheses are allowed in the Logic text box Also you can use a criterion more than once in the Logic field For example the expression 1 AND 2 OR 1 AND 8 entered in the Login field would find database entries that satisfy either criteria 1 and 2 or criteria 1 and 3 Search Pathways Create Subset x Search Conditions C1 Component Name List Condition C2 Component GO Annotation apoptosis inhibitor activity GO Add Single Condition ogical Condition Association And Custom Mg All Pathways OOI Demo Pathways Gi Metabolic Pathways Gi Signaling Pathways EO d al EA ose He Figure 3 55 Search Create Subset wizard listing two logical search conditions A text string cannot contain the character T Check the checkbox by one or more subsets from the Search in Subset folder Select the All Reactions Components Pathways subset checkbox to search all database objects of the selected type Click Next The search is started Depending on the search complexity and database size the search may take several minutes Search Results 58 When the search is complete the Search Results screen lists the objects that meet the search conditions Figure 3 57 Working with Pathways Chapter 3 Single Condition Search The Name column lists each returned object by nam
94. and Hogue CW 2001 BIND The Biomolecular Interaction Network Database Nucleic Acids Research 29 1 242 45 Licensing Information BioCyc Description URL Reference There are no license conditions attached to the use of the BIND database All data records in the public BIND database are in the public domain A collection of Pathway Genome Databases make up the BioCyc Knowledge Library The genome and metabolic pathways of a unique organism are represented in each database in the BioCyc collection The MetaCyc database however is an exception in that it is a reference source on metabolic pathways from many organisms The above text is paraphrased from the BioCyc website listed below http www biocyc org Karp P D Riley M Saier M Paulsen I T Collado Vides J Paley S M Pellegrini Toole A Bonavides C Gama Castro S The Ecocyc database Nucleic Acids Research 30 1 56 2002 Licensing Information 200 http www biocyc org Transpath Description URL Reference References Appendix C The TRANSPATH Professional database is a repository of data for molecules participating in signal transduction and the reactions they undergo thus spanning a complex network of inter connected signalling components TRANSPATH Professional focuses on signalling cascades that aim at transcription factors and thus alter the gene expression profile of a given cell TRANSPATH Professional is the resource of c
95. annotations tab for each Check the Organisms tab for each to see if any objects have current organism annotations Close the dialog box Now select Manage Gene Ontology gt Populate Organism Attribute In the Populate Organism Attribute dialog box that opens check the All Components subset In the Attribute Type select Known In This selection means that an object is definitively known to be in certain organisms locations but it cannot or has not been definitively determined whether it is known to be in other organisms locations Click Populate With this feature activated if there any taxonomy GO annotations for components that already have GO annotations these will be added to the Organism tab Check the Organism tabs for the 3 objects again to verify that this operation was executed For more information about working with GO Annotations refer to the following topics e Customize gene ontology display on page 22 e Search Database by GO Annotation on page 61 163 Vector PathBlazer 2 0 User s Manual 164 CHAPTER WORKING WITH GENE EXPRESSION DATA This chapter describes how to integrate Vector PathBlazer with Vector Xpression and other expression data Additionally it describes overlaying gene expression data on the topology of a pathway Topics in this chapter include e Introduction to Expression Data Import and Display on this page e Interaction Between Vector PathBlazer 2 0 and Vector Xpression 3 1 on page 166 e Cr
96. anual Gene Ontologies Vector PathBlazer allows you to import Gene Ontologies pre defined classifications of Genes and Targets that you download and save locally from the Gene Ontology Consortium For more information see Chapter 7 Gene Ontologies From PathBlazer you can assign selected Path Blazer objects to these ontologies and they become associated as gene annotations Integration with Vector Xpression 3 1 Vector PathBlazer 2 0 includes tools for directly accessing expression data in Vector Xpression 3 1 Vector Xpression 3 1 contains tools for sending gene expression data directly to Vector PathBlazer 2 0 For more information see Chapter 8 Working with Gene Expression Data CHAPTER WORKING WITH PATHWAYS This chapter describes PathBlazer Viewer the main viewer in Vector PathBlazer that is used to view draw and manage pathway data in the database Drawing pathways is described in Chap ter 3 Working with Pathways Topics in this chapter include Launching PathBlazer Viewer on page 10 Elements of PathBlazer Viewer on page 11 Working with Pathways in the Graphics Window on page 13 Working with Pathways in the Database Explorer on page 31 Annotating Pathways Components Experiments Reactions and Connectors on page 37 Saving PathBlazer Components Reactions and Pathways on page 46 Opening Crosslinks to External Databases on page 52 Searching the Database on page 53 Printing and Saving Images on page 63 Vect
97. ard select the xml file for import by clicking the Browse but ton locating the corresponding file in the Open dialog box and clicking Open The com PathBlazer Import Select source file E ARITU Hee nda db mdb d Back Ment gt Cancel Help Figure 4 20 Proprietary Import dialog box for selecting XML source file 5 In the Merge Options dialog box select the options appropriate for merging the data See Merge Option Dialog Box on page 67 for more information Click Next to continue The data loads while a monitor displays allowing you to follow the import process An import log summarizing import results displays when the import has been successfully com plete 6 To stop the import click Cancel Click Close 106 Importing Data Chapter 4 Pre Defined URLs some pre defined URLs are automatically associated with imported entries The associated link depends on the type and source of entry For example a BIND component is associated with a link to the BIND database by the entry value of the component Pre defined URLs are listed in Table 4 7 with the name that is displayed for each link in the program Examples are shown with an actual entry value but this value depends on the entry number of each component and reac tion Description URL Display Name Bind Component http bind ca cgi bin bind dat BIND Protein Link aget get tin dex amp text_query s amp iid_cb 4 amp mci d_cbh 16 amp pid_cb 8 amp npp
98. as C My Documents My PathBlazer Data PathBlazer_demo_db mdb To view another database select the appropriate mdb file Important If you have a PathBlazer 1 0 database when you choose to open that database in PathBlazer 2 0 you will receive a warning saying that the database will be automatically converted to Path Blazer 2 0 format Click OK Then be patient as the database conversion may be somewhat time consuming Backing Up the Database At certain points in your data collection and annotation process you may want to take a snap shot of your database or you may want to create backups of one or more databases Since all of the data is located in one file for a particular database you can simply copy the associated mdb file rename it and relocate it to an archive or backup directory Elements of PathBlazer Viewer PathBlazer Viewer is the main interface in Vector PathBlazer where pathways are built viewed drawn annotated and searched PathBlazer Viewer is made up of a menu bar and a general toolbar at the top of the window The Pathway Viewing Area displays in the middle of the window and the Database Explorer and sta tus bar display at the bottom of the window Figure 3 2 The status bar displays the current database settings such as the number of items currently displayed It can be hidden from view by selecting View gt Status Bar Divider bars separate different areas of the screen and when the cursor turns to a double h
99. associated with a reaction including Constants Condi tions Locations Organisms Cross Links and Pathways The properties of reactions and connectors can be modified from the Text View tab by selecting either a reaction or connector and selecting Reaction Properties or Connector Properties respectively from the shortcut menu Fructose 6 phosphate Glucose 6 phosphate 4 I Constants 2 delta G 1 7 kJ mol I Conditions C Locations I Organisms A Cross Links I Pathways Glycolysis B Glucose 6 phosphate isomerase Figure 3 26 Reactions folder in the Text View tab Components folder contains subfolders for each separate component in the pathway A com ponent is represented by the D icon and contains each reaction in which it is included Figure 3 27 The properties of components can be modified from the Text View tab by selecting a com ponent and then selecting Component Properties from the shortcut menu G E Components FH Hexokinase Ea glycolysis rxn Glucose ATP gt Glucose 6 phosphate SES abe SIDI SNEOUTEZ Glucose 6 phosphate 4 bo glycolysis_rxnZ Glucose ATP gt Glucose 6 phosphate a EA dlhvcolysis_rxn9 Glucose 6 phosphate gt Fructose 6 phosphate SDO Fructose 1 6 bisphosphate Ik SO bo glycolysis _rxn10 Fructose 1 6 bisphosphate gt Dihydroxyacetone phosphate Glyceraldehyde 3 phosphate glycolysis _rsn4 Fructose 6 phosphate ATF gt Fructose 1 6 bisphosphate ADF d ATP C10H1
100. at the component is not already in the database it opens a wizard that assists you in creating the new component including naming and annotating it Use the fol lowing steps to draw and annotate a new component 1 Select a shape in the Palette window and move the cursor to the Graphics window The cur sor changes to the symbol TTU Click anywhere in the Graphics window to insert the shape When the shape is initially inserted it is called lt UNNAMED gt by default The cursor remains a wand until you either click another shape or line in the Palette window click on one of the buttons in the Graphics toolbar such as the arrow icon E Or press ESCAPE To assign a name to the shape click the arrow icon on the toolbar double click on the shape enter a new name and press enter If the name matches an object in the database by primary name or by synonym the object is automatically named by the primary name If the entered name does not match an object already in the database or a synonym of an object see preceding page a dialog box opens allowing you to select among several 113 Vector PathBlazer 2 0 User s Manual options related to naming the new shape Figure 5 3 Only options appropriate for your new object type are available New Renamed Component Select Option E EA AN component with name new enzyme has not been found in the Database Please select one option Look for components with similar n
101. at you received when purchasing Vector PathBlazer or Download the Vector PathBlazer 2 0 Installation and Licensing Guide from the Invit rogen InforMax website www informaxinc com or Vector PathBlazer 2 0 User s Manual See the Appendix A License Manager in this user s manual e To start Vector PathBlazer refer to Launching PathBlazer Viewer on page 10 e To learn various methods of opening and using of Online Help refer to Using Online Help on page 3 Manual Purpose The purpose of this manual is to provide you with information and instructions for using Vector PathBlazer to view build and analyze pathway and protein protein interaction data Manual Contents This manual is organized into chapters that provide information about how to use the program and appendixes that provide supporting information Chapter 1 this chapter contains a brief introduction system requirements and conventions used in the manual Chapter 2 provides an overview of Vector PathBlazer features Chapter 3 describes how to view manage and work with pathways in PathBlazer Viewer Chapter 4 describes how to import public and proprietary data into Vector PathBlazer Chapter 5 describes how to draw pathways de novo in PathBlazer Viewer Chapter 6 describes how to use Vector PathBlazer to suggest new pathways and protein protein interaction networks from known components and reactions Chapter 7 describes gene ontology terms and annotation
102. ata import 65 DIP 97 DTD for importing proprietary data 191 expression data 168 expression template 171 gene ontologies 153 gene ontology terms 154 KEGG 72 PPI 100 pre defined URLs 107 proprietary data 102 root folder description 67 session monitor 70 source file description 67 steps for general import 66 Import Manager description 66 In description 56 Interaction generality definition 137 setting for pathway building 137 Interactive Zoom 18 Intersection of subsets 34 K KEGG Compound file 73 description 72 Enzyme file 75 Genome file 78 import instructions 79 import logic 73 Reaction files 77 source files 72 Known In description 56 L Label changing graphical properties 132 creating 131 deleting 132 description 131 Launching PathBlazer Viewer 10 Layout circular 25 dialog box 25 hierarchical 25 symmetrical 25 Layout properties 25 License Manager 183 configuring dynamic license 187 configuring trial license 187 resetting static 186 214 Licenses Vector Xpression 183 License status 183 Linking expression data and components manually 171 expression data to pathway components automatically 166 Log file contents of 72 permanent 71 Logical conditions for database search 58 M Manual conventions 4 Marquee Zoom 18 Master View copying as Alternate View 31 creating new Alternate View 30 description 12 opening a pathway in 14 viewing pathways graphically 14 mdb file backing up 11 creating new database
103. ate Delete Figure 8 7 Expression Import Template Manager 170 Working with Gene Expression Data Chapter 8 2 To add more component gene pairs to the template select a template name from the Tem plates list box and click Edit The Map screen opens displaying the current mapping between components and gene names IDs Figure 8 8 Use the instructions starting on step 2 on page 172 through step 5 on page 173 to modify the map Note Click on the Component or Gene column headers to sort by one column or the other Pathway Components E Component Gene Hexokinase HXK1 Glucose 6 p EGI Phosphofruc PFK1 Aldolase EPAI Triose phos TPI Glyceraldeh TDH1 Phosphoqly PGK1 Jej eio TT dr Add m Link Orphan Genes Relink All Genes Using DB Links Using Names and Synonyms Using DB Links Using Names and Synonyms Cancel Help Figure 8 8 Editing a template 3 Click Finish to execute the edit This returns you to the Expression Import Template Man ager 4 To add a new template click Add The Define Source screen opens where you select an expression data file Follow the steps starting with step 2 on page 168 5 To duplicate a template select a template from the Templates list box and click Duplicate Enter a new name for the template and click OK The new template is added to the list box You can then edit the mapping by clicking Edit 6 To delet
104. athBlazer Synonym All other entries are imported to the Synonym field Formula Chemical formula of the com Chemical Formula pound DBLinks Link information to other data CrossLinks bases Currently only contains a link to CAS Chemical Abstracts Literal value of this field for example CAS 64 Service and PROMISE Pros 17 5 is imported as a crosslink of type Data thetic groups and Metal lons in base Protein Active Sites Database A crosslink of type URL is automatically cre ated for all KEGG components A link is made to the URL http Awww genome ad jp dbget bin www_bget compound lt entry gt where lt entry gt is the value of the ENTRY field in the component file A list of pre defined URLs is listed in Pre Defined URLs on page 107 Table 4 2 Imported attribute fields in the Compound file The ID number in the Entry field is used to link a reaction to a component but is not actually parsed into Vector PathBlazer This is described in further detail in KEGG Reaction Files on 74 Importing Data Chapter 4 page 77 Also the attribute Datasource is automatically defined as KEGG for all imported KEGG components KEGG Enzyme File The Enzyme file is a collection of all known enzymatic reactions classified according to the nomenclature of the International Union of Biochemistry and Molecular Biology IUBMB Each Enzyme entry is identified by an EC Enzyme Commission number and contains attrib
105. athBlazer would search the database for glucokinase Three options can be returned from the search Reminder Note 1 The program finds a component in the database that has the primary name glucokinase and names the shape that is the component drawn in the Graphics window Glucokinase You have not created a new component by drawing it and then selecting its name from the database you are simply referencing a component that was already in the database The program finds a synonym component in the database that has the primary name hex okinase and the synonym glucokinase You are offered the option to make glucokinase the default name in the database or alternatively to make glucokinase the display name within the current pathway only If you decide to leave the default name for the component hexokinase you can change the name later by selecting it then choosing Change Component Display Name from the shortcut menu In the dialog box that opens you must select from among the displayed identities Synonyms currently in the PathBlazer database You cannot assign any other name to the component In the dialog box you can specify whether the new display name is for the current pathway only or to be displayed in all pathways henceforth The program does not find a component named glucokinase by primary name or synonym names the shape Glucokinase and creates the corresponding component in the database If the program determines th
106. athways Create Subset b xj Search Results Name sE Pentose_pi Pathway d Gluconeogenesis Pathway d G protein Stimulatory Ge d Tricarboxwlic Acid Pathway d Glpcolysis Pathway meta d Glpcolysis Pathway d EGF Signaling Pathway G NAD Results Si Eu NADH Results Si GAME Results Si Gull NADPH Results Si Ell COZ Results Si E FADH2 Results Si ATF Results Si El ADP Results Si E NADP Results Si Gl H20 Results Si ll GDF Results Si ed T items in selected folder Append selected items to subset Save the search results as a subset Close Help Figure 3 57 Search Create Subset wizard listing search results 8 There are several options for adding search results to subsets Add selected search results to an existing subset by selecting one or more entries from the list To select consecutive objects in a list select the first object press the SHFT key and select the last object To select non consecutive objects press the CTRL key and select the 59 Vector PathBlazer 2 0 User s Manual objects Click Append selected items to subset to open the Append to Subset dialog box Figure 3 58 Click the sign to expand the displayed folder for example Components select an existing subset and click Append Append to Subset 3 x El Pathways oof All Pathways El Demo Pathways d fall Metabolic Pathways ve Signaling Pathways Subset Nam
107. avine a PW File tothe Dalaba Eend a a e aaa a a a 51 Opening Crosslinks to External Databases rra 52 Searc hne TMG Database aeon aate aittai 53 Finding an Object ma B ar 53 Searching Objects in the Database and Creating Subsets sa 54 Search Database by GO Ammotation cccccccccsesessncccsnennoncccsceceseesesessessevssecenancstececceterteceseesens 61 Primi Ger Har 63 Pannie ANN A TAN akabatuta 63 DV MS Ah AAO Cicada are ootes Aen toca eae bateak ideiatik EE 63 Chapter 4 IMPONG BEZE 65 Introduction to ilar BA 65 About Vector Path Blazer Data Import giarik atazan 66 Import Module and EGO raa aiak iar aate a eitzie 66 Root Polder or Source File Dialog Saba 67 Merge Option Dialog Ba 67 Iporo esso MOnO EAEE 70 PaihnBlazer Sa BUNOS oreari e a a A 71 Path Blazer LoS BIZ 71 Higie KECE EO 12 KEGG SOURCE EAE d EEG TMPO E eiza 73 KEG Compound ek 73 KEGG ENV ME a UAE 75 KEGG RGACH On RUE Td KEGG Cenome A UAE 78 lnstructrons Tor Imporine EAEE 79 Isis BIND ata A 80 EAR pea bian aA 81 BIND IMPO Pear 83 Instructions for Importing BIND agurra aaa aiii teetara 84 Importing BoC ye Data aaen e aate 85 BC CSO ezk aA 86 BioC ye mipor Ee 86 Table of Contents Bio ye Component PF NCS gt soshy dn cial caret a E dus eh toca vada ede dao lace eaeleeeatess 87 PIO ye Reaction Si eNA 89 BO Gy Path ays aN 90 Instructions tor Importing Bio Cy 6 Data arterat ratutako ika areta 92 diges Tans B KAE 93 Trans Pali Source UAE 93 Instructions for Im
108. bhl into ZI Cdupl 1 Conflicts found while merging component ADE into ADP Organism contradiction Known In E coli H 0157 dropped because of Only In E coli conflicts found while merging component ATP into AIE Organism contradiction Known In E coli H 0157 dropped because of Only In E coli Merging component trpL into trpl Cdupl 1 Merging component fadb into TAO Cdupl 1 Merging component NAD into NAD Merging component crp into crp dupl 1 Merging component MADE into NADP Figure 4 6 PathBlazer permanent log file 71 Vector PathBlazer 2 0 User s Manual The file an example of which is in Figure 4 6 is a wrap around file when it reaches a certain size limit the older information gets removed The following information is stored in a log file e Batch attribute change when attributes are changed in batch mode all changes are recorded e Import events component merge and component renaming during import e Merge of components by manual means after data import Importing KEGG Data The KEGG Kyoto Encyclopedia of Genes and Genomes database is a collection of interacting molecules and genes based on the current knowledge of molecular and cellular biology Data in the database is also linked to the gene catalogs produced by genome sequencing projects A complete description of the contents of the KEGG database as well as licensing information is available at htt
109. bstances that cannot be clas sified as nucleic acid or enzyme These components are identifieid by their UNIQUE ID Com pounds have information about their type commonly used synonyms atomic charges chemical formulae links to external databases etc The following is an example of components extracted from the Ecoo15 Cyc compounds dat file The values shown in bold are parsed by PathBlazer 2 0 The chemical formula is reconstructed For a component below the formula will be C12H17N401S1 HTML specific tags like lt SUB gt and lt SUB gt are removed from names The synonym of the component below is Vitamin B1 UNIQUE ID THIAMINE TYPES Vitamins COMMON NAME thiamine ATOM CHARGES 9 1 CHEMICALFORMULA C 12 CHEMICALFORMULA H 17 CHEMICALFORMULA N4 CHEMICALFORMULA 01 CHEMICALFORMULA S1 DBLINKS CAS 59 43 8 MOLECULAR WEIGHT 265 352 SMILES c1 c cne C n1 C n 1 2 c C c sc2 CCO N SYNONYMS thiamin SYNONYMS vitamin B lt SUB gt 1 lt SUB gt File enzymes col This file contains information about enzymes This is a tabular format file A one line excerpt for glucokinase is given below A component in PathBlazer named ENZRXN7E 124 with the synonym glucokinase and type Enzyme is created The annotations store information that this enzyme catalyzes the reaction beta D Glucose ATP beta D glucose 6 phosphate ADP This enzyme is found in TREDEGLOW PWY and acts as monomer ENZRXN7E 124 glucokinase amp beta D g
110. cally In some cases the downloaded files are zipped and you must unzip them before you can proceed with import Once you have done so the PathBlazer Import tool is used for specifying source files parameters where appropriate and importing the data When you import public data PathBlazer Import automatically converts the files to Vector PathBlazer XML format for you When you import proprietary data you must first format the data in XML format according to the Vector PathBlazer Document Type Definition DTD before you can import the data For information about doing so see Appendix B DTD For Data Import Every import session follows the same general steps no matter what kind of data is being imported 1 Open the PathBlazer Import Module dialog box where you select the datatype to be imported 2 Open the Root Folder or Source File dialog box where you locate and select the root folder or source files of the data Open the Merge Option dialog box where you specify how data merge is to be addressed 4 Execute the data import A monitor allows you to follow the import process an import log summarizes the import statistics Each part is described in detail in the following subsections and directions specific for each datatype are described in even more detail in the datatype subsections Import Module and Description 66 Import Module The Import Module field allows you to choose commonly downloaded public or proprietary da
111. cess by choosing an example of a KEGG reaction in the Graphics window Similar to BIND DIP data contains only information about interactions between two components that is proteins There are no predicted products and each DIP reaction is represented as a protein protein interaction Importing PPI Data When a sequence of a protein is known clues to the correlation of the protein sequence and its structure to its functionality begin to unfold Domains usually the functional regions of a protein molecule can interact with a wide range of cellular objects including domains on other proteins The interactions of proteins with each other and the strength of the interactions helps scientists to visualize and correlate protein pathway data and chart protein pathways within cells PathBlazer allows you to view a network of proteins linked by their domains to ligand interac tions You can display analyze and manipulate a graphical representation of a PPI protein pro tein interaction network PPI data import is a simple process in PathBlazer Prepare the data in a 3 column tab delimited file with a column for each protein A protein B and the strength of the interaction affinity Instructions for Importing User PPI Data You can import data either into the default PathBlazer database or into a new separate database you create before the data import To create a database see Creating a New Database on page 10 100 Importing Data Chapt
112. cesses and interactions through which the individual catalogued parts interact and function It is through finding important net works among the various parts under normal and disease conditions that the complex regula tory pathways of biology can be understood at a level to effectively modulate them In this effort it is critical to draw on all available knowledge and arrive at a solution that combines well known biological facts with new less understood areas Vector PathBlazer can aid in developing test able hypotheses that can be used to extend biological knowledge Main Features The key features of Vector PathBlazer are e stores molecular interaction data from proprietary and public data sources e imports both proprietary data and public data including KEGG BIND DIP TransPath PPI and BioCyc databases e stores components reactions and pre assembled pathways separately in a proprietary data model Vector PathBlazer 2 0 User s Manual e draws component reactions and pathways de novo e assembles potential networks across different data sources e assembles pathways and protein protein interaction networks interactively in a step wise manner using query and filter options and displays resulting pathways and networks in a graphical view e uses Interaction Generality as a measure to enrich for biologically relevant protein pro tein interactions e annotates pathways reactions and components e links to sequence records
113. ch annotation field is described in Annotating Pathways Components Experiments Reactions and Connectors on page 37 47 Vector PathBlazer 2 0 User s Manual 48 In the Save Pathway Organisms screen associate one or more organisms with the path way by clicking Add Save Pathway Organisms b 3 E x d Pathway Iar o O Organisms Locations Reference Cross Links Fa Reaction gluco rend d Components KO Properties Constants Conditions Organisms Locations Cross Links de Pathways Complete Add Edit Delete lt Back Save Cancel Help Figure 3 40 Associating a pathway with one or more organisms In the Organism dialog box select a Type and a Name from the drop down lists Figure 3 41 You can also type in the name of an organism if it is not listed in the drop down list Click OK Select an associated organism and click Edit to modify it Click Add to add another organism Click OK Click Next or click a hyperlink in the left pane to move to the next Pathways annotation screen Continue annotating the pathway from the remaining screens Figure 3 41 Assigning organism attributes to a pathway If you advance the Pathway screens in sequence the Reactions screens display next For each reaction the Save Reaction Components screen displays first and contains a list of the components in the reaction Figure 3 42 The Name column displays each component and the remaining columns display information
114. ch you can edit Click Next to continue The next several dialog boxes display annotations for each component with each dialog box assuming the name of the annotation Component Locations Organisms Compo 45 Vector PathBlazer 2 0 User s Manual Note nent Crosslinks Synonyms and GO Annotations You can edit any of these annota tions Continue to click Next to continue to each succeeding dialog box 6 Before you complete the merge a Merging Components dialog box describes the merge that will occur which component will be deleted from the database and which will be retained as well as how components have been renamed where appropriate Click Finish to execute the merge If there are conflicts in the organism or location attribute an error message describing the con flict displays when you try to continue Components and reactions can also be merged automatically during import For more informa tion see Merge Option Dialog Box on page 67 Saving PathBlazer Components Reactions and Pathways When you create or modify a component in the Graphics window you are automatically prompted to name annotate and save the component If you decide not to save the pathway in which a component is drawn the component is still saved to the database Details for saving new components are described in Drawing a New Component on page 113 Pathways and reactions are saved differently than components New or modified pathways and reactions
115. comes extremely complicated in terms of the numbers of components and reactions or you might be focusing on a specific part of a pathway and cannot see another part of interest in the same view To locate a specific component or reaction in a pathway displayed in the Graphics window use the following steps 1 Select the window that contains the pathway you want to search If pathway windows are tiled or cascaded Window gt Tile or gt Cascade the currently selected window displays a blue title bar Select Edit gt Find 2 Inthe Find Pathway Item dialog box select either the Component or Reaction radio but ton Figure 3 48 When the Show AI radio button is selected the list box shows all compo nents or reactions in the pathway by name To filter components reactions by name select the Show only items containing text radio button and enter text that matches the items you want to see Select the component reaction you want to search for in the List box and click OK Find Pathway Item x Pathway ltem Type Gz Component Reaction f Show All Show only items containing text 6 70 rrethylene THF arminomethyltransterase T protein tetrahydrofolate dependent LUA H H20 L qlycine L serine NADA NADH NH3 Cancel Help Figure 3 48 Finding a component or reaction in a pathway 53 Vector PathBlazer 2 0 User s Manual 3 The component reaction is centered in the Graphics window and is select
116. construct known pathways and use known information about reactions to discover novel pathways and networks Pre Loaded Data To aid you in learning to use Vector PathBlazer several different pathways have been entered from the literature and are pre loaded in the Vector PathBlazer database for your use The fol lowing pathways are pre loaded in the default database that is installed when Vector PathBlazer is installed e Metabolic Gluconeogenesis Glycolysis Pentose phosphate Tricarboxylic Acid TCA e Signal Transduction TNFR Wht EGF Signaling The pathways include the associated components linked into the appropriate reactions See Appendix C for references associated with these pathways Since all data records from BIND Biomolecular Interaction Database are in the public domain the BIND interaction database is also pre loaded in the Vector PathBlazer database The BIND database is loaded as a set of components and reactions in Vector PathBlazer For more infor mation see Chapter 4 Finally a set of expression values from multiple expression runs that map to the gene products of the enzymes in the glycolysis pathway is pre loaded The file containing the values is also included in the default database directory C VNT Database Pathway DB DeRisi_glycolysis_exp_import txt This data is used in Chapter 8 to demonstrate how expression values are mapped on the topology of a pathway Vector PathBlazer 2 0 User s M
117. contains the complete genome sequence of E coli and describes the nucleotide position and function of every E coli gene EcoCyc also describes E coli operons promoters transcription factors and transcription factor binding sites A complete description of the contents of BioCyc licensing information as well as downloadable databases are available at www biocyc org and _ http biocyc org flat file reg shtml Reference and licensing information is also available in Appendix C To download BioCyc databases you can select the specific databases and download them one by one from the BioCyc website or they can all be downloaded together Refer to the website for download instructions The data files from which BioCyc data are imported into PathBlazer are provided in a defined format as specified by BioCyc http org ai sri com ptools flatfile format html PathBlazer 2 0 was specifically designed to import only those files defined by BioCyc in their Flat File Format 85 Vector PathBlazer 2 0 User s Manual BioCyc Source Files Import of BioCyc data will be described using the Ecoo15 Cyc file the database that contains information about E coli H 0157 Download either the Ecoo15 7Cyc flatfiles zip or Ecoo15 Cyc flatfiles tar z according to your preference and unzip it In your root folder the following source file s will display bindrxns dat classes dat this file is not used for BioCyc import compounds dat dnabin
118. ctional connector are displayed as individual objects in a reaction Protein protein interac tions with non directional connectors can also be displayed Experiment or Runs Project A collection of Expression Runs combined for simultaneous analysis Expression Run In the context of Vector Xpression an array of numbers equal in length to the number of Expression Genes that were measured that corresponds to the expression val ues obtained when an Expression Target is put through the measurement oprotocol I E a microarray hybridization or SAGE run Interaction Generality Number of proteins that directly interact with the target protein pair minus the number of proteins that interact with more than one protein plus one A lower generality score indicates a more biologically relevant protein protein interac tion Label Displays additional information or titles on a component reaction node or con nector in the Graphics window Master View Tab in the Graphics window in which a pathway and its associated data is viewed in graphical format as opposed to text format 209 Vector PathBlazer 2 0 User s Manual 210 Metabolic View Type of view where catalytic reactions those that involve an enzyme and a bidirectional connector are not displayed as individual objects in a reaction Instead an enzyme displays as a label of the reaction node and the connector does not display Protein protein interactions with non directional conne
119. ctors cannot be displayed in this type of view Non strict Search Search term that returns objects that are assigned the value of In or Known In for Location and Organism annotations Also returns objects that are assigned no value for Location and Organism annotations Pathway One of the main database object types that is made up of one or more reac tions linked together Different types of pathways can be modeled in Vector Path Blazer including metabolic and signal transduction pathways Pathways can also be made up of networks of protein protein interactions Pooling Refers to displaying just one time a component that occurs more than once in a pathway In the Graphics window multiple connectors are drawn from the one object to the reactions in which it is involved Protein Protein Interaction Reaction between two proteins Reaction Node Graphical representation of a reaction in the Graphics window Reaction One of the main database object types that is made up of groups of one or more components that undergo a transformation or interaction Strict Search Search term that returns objects that are assigned the value of In or Known In for Location and Organism annotations Subset A type of container that contains references to objects in the database and can be used to group objects with one or more properties in common Synonym Alternate name or alias of a component Template Defines the mapping between a set of gene names
120. cts with a particular ontology classification You can also perform database searches for objects anno tated with specific GO terms The GO annotations display on the Properties GO Annotations tab for Components Reactions or Pathways For more information see Annotation Fields for Components Reactions and Pathways on page 39 Working with Gene Ontology Terms Importing Gene Ontology Terms After you have downloaded the gene ontology terms dictionary from the Gene Ontology Consor tium website see previous section you can import the file into PathBlazer Use the following steps to perform the import 1 Open PathBlazer 2 Before launching import close all PathBlazer display windows 3 Select Tools gt Manage Gene Ontology gt Import Terms 154 Gene Ontologies Chapter 7 4 In the first Gene Ontology Import dialog box that opens click the Browse button to locate and select the file you want to import Figure 7 1 For GO terms the file must have an xml extension Gene Ontology Import B b Select Gene Ontology Terms Import Options Select source file E Browse Cancel Help Figure 7 1 Gene Ontology Import Terms dialog box 5 Click Next At this point the GO terms will be loaded The screen displays a monitor showing the import progress After this import procedure you can proceed with importing the gene ontology anno tation file See mporting Gene Ontology Annotations on page 159
121. d build pathways it is important to first understand how path ways reactions experiments and components and the relationships between them are repre sented in Vector PathBlazer Pathways the reactions that make up a pathway and the components that make up a reaction can be graphically or textually displayed in the Graphics window 13 Vector PathBlazer 2 0 Users Manual Opening a Pathway Note Pathways are either stored in the database that is an mdb file or an exchangeable XML file having the extension pw A pw file is a mini database that stores an individual pathway its associated reactions and components and all annotations These files can be used to share specific pathways with colleagues who also have Vector PathBlazer See Saving a pw File to the Database on page 51 for instructions on how to save a pathway as a pw file Open a pathway stored in the database by locating the Pathways folder in the Database Explorer and double clicking on All Pathways In the Contents Pane all pathways in the data base display Locate a pathway in the Name column and double click on it A graphical repre sentation displays in the Master View tab of the Graphics window For information about the Text View tab see Viewing Pathways in Text Format on page 28 Initially the elements of the pathway are sized so you can easily see them in the Graphics window Figure 3 7 However the entire pathway may not visible Use the scroll ba
122. d selecting View gt Object Properties or Object Properties from the shortcut menu In the Object Properties box that opens Selected Graph Properties displays in the drop down list at the top Figure 3 21 You can also display the graph s properties when an object s properties are displayed by selecting Selected Graph Properties from the drop down list The Properties box for a graph summarizes the total number of reaction nodes connectors and labels in the pathway However the only graph property you can change from this box is the background color Click the Browse button in the Background Color field and select a color from the palette lz Object Properties Selected Graph Properties D Background Color Figure 3 21 Object Properties box for a graph Graphical Layouts Graphical layouts are pre defined orientations that can be applied to a pathway s graphical view There are three layouts that can be applied to pathways in the Graphics window Circular Hier archical and Symmetrical When a layout is applied the pathway elements are rearranged according to the settings for that layout Apply a layout e by selecting Layout gt Circular Layout or clicking the EO button on the Graphics tool bar Working with Pathways Chapter 3 e by selecting Layout gt Hierarchical Layout or clicking the th button e by selecting Layout gt Symmetric Layout or clicking the E button Note When any of these buttons is clic
123. deleting an object from the Database Explorer the following rules apply e The All Components Reactions Experiments Pathways subsets contain the original or primary copy of any database object When a copy is made of one of these objects and placed in a subset the subset contains a reference or shortcut to the primary object and the copied reference is named identically to the referenced object e When an object in the database is renamed or its properties are changed the primary object and all references to that object are also changed regardless of whether the object is changed from the primary copy or a referenced copy If a component is refer enced by a reaction the name of the component is changed in the reaction If a reaction or component is referenced by a pathway the name of the component or reaction is changed in the pathway e When an object is deleted if it is a reference to the primary object that is if it is not deleted from the All Components Reactions Experiments Pathways subsets then the reference is deleted but the primary object is not A primary object can only be deleted if it is not referenced by any copies To permanently delete an object it must be deleted from the All Components Reactions Experiments Pathways subsets deleting it from a subset only deletes the reference If a component is included in one or more reactions or pathways it cannot be deleted until it is removed from all reactions and pathways in
124. dialog box can be used to save pathway and reactions to either the database or to a pw file and can also be used to annotate pathways and reactions similar to annotating components A pw file is an XML file in which individual pathways are saved to the local file system These files can be used to archive and share pathways with other Vector Path Blazer users The Save dialog box is divided into two parts a wizard displays on the right side and con tains Back and Next buttons for advancing through the screens in sequence The left side contains hyperlinks for jumping to specific screens The left side is also divided into two parts The hyperlinks under Pathway are for naming and annotating the current pathway Each reaction in the pathway displays further down under Reaction lt Reaction Name gt The hyperlinks under a reaction name are for naming and annotating that reaction A sepa rate screen displays with the appropriate annotation for each hyperlink To save the pathway to the database select the Database radio button and select a specific subset in the drop down menu If you do not select a subset the pathway is saved to the All Pathways subset To save a pathway to a file select the File radio button and click the Browse button In the Save as dialog box that opens navigate to the location where you want to save the file and enter a name in the File name field All files are saved with a pw extension to indi cate they a
125. dsites dat ecobase ocelot this file is not used for BioCyc import enzrxns dat enzymes col genes col genes dat pathways col pathways dat promoters dat protcplxs col proteins dat protseq fasta this file is not used for BioCyc import pubs dat reactions dat regulons dat terminators dat transporters col transunits dat BioCyc Import Logic 86 1 Pathblazer component information is assembled from the following files compounds dat dnabindsites dat enzymes col genes col genes dat promoters dat protc plxs col proteins dat regulons dat terminators dat transporters col transunits dat Reaction information is gathered from findrxns dat and reactions dat Pathways information is loaded from pathways col and pathways dat The data files from which BioCyc data are imported into PathBlazer are provided in a defined format as specified by BioCyc http org ai sri com ptools flatfile format html In this section are examples of the data from the public dataset to show the files and fields used to populate Vector PathBlazer during import PathBlazer 2 0 was specifically designed to import only those files defined by BioCyc in their Flat File Format Files marked with asterisks are used to import EcoCyc and MetaCyc databases and are not described in this manual Importing Data Chapter 4 BioCyc Component Files File compounds dat The compound data file is a collection of organic and inorganic su
126. e e Interactions contain two BIND objects A BIND object describes a molecule of any type e Molecular complexes define and describe the interactions between any two mole cules The majority of stored information is between proteins DNA and RNA e Pathways define collections of more than two interactions Each object is composed of various component and descriptive objects which can be imported into Vector PathBlazer as annotations The data that can be imported into the Vector PathBlazer database is included in three division files One or more of the files are available for download one by one at ftp ftp bind ca pub BIND DB archive These files contain information about components and reactions Download the BIND_Interaction xml gz file to your local file system and then extract the file with a program such as WinZip Once extracted the file BIND_Interaction xml is created A partial example of the contents of the BIND_Interaction xml file is shown below with an expla nation of how the information in the file is parsed into Vector PathBlazer A list of reactions with the corresponding components is created in the database from the file The BIND Document Type Definition DTD can be found at ftp ftp bind ca BIND Spec xmidtd The values that are directly parsed are shown in bold XML Source lt BIND Interaction gt lt BIND Interaction_tid gt lt Interaction id gt 301 lt Interaction id gt lt BIND Interaction_t
127. e Select Don t Pool Components in Subset and select the Small Molecules subset 9 Select the All Reactions subset 10 Set Direction to Ignore 11 Set Interaction Generality to Unlimited The Build a Pathway dialog box should look similar to that in Figure 6 9 Build a Pathway E E i x Fath Build Pathway I from Component ja from Pathway Pathway glycolysis 2 steps Browse Component Subsets le Ignore Paths through these Components bi Small Molecules Build Fathway to Component ld to Pathway I Don t Pool Components in Subset TNFR Signaling Pathway Browse bi Small Molecules I Hide these Components Build Pathway through Component fructose 6 phosphate OA Choose Component Subset Include Reactions from Subsets KL Reactions GI All Reactions Si glycolysis I Show only connecting components Calculate critical points Connection Length Pathway Direction Maz Number of Steps Extra Steps Direction Interaction Generality fi 0 E jo E Ignore E Unlimited E bak i Cancel Help Figure 6 15 Building a link between two pathways 12 Click OK to start assembling the pathway 149 Vector PathBlazer 2 0 User s Manual Assembled The result displays a complex pathway starting with the Glycolysis 2 Steps pathway and a three Pathway step link proceeding to the TNFR Signaling Pathway Figure 6 16 The beginning pathway is shaded light blue the ending pathway is shaded pink The star
128. e Help Figure 7 4 Linking to external websites from the GO Browser QuickGO AmiGO MGI EP GO CGAP Their description is located at the following link http Awww geneontology org GO tools html Note This dialog box is similar to that used for manually adding and editing gene ontology terms as described in the following section Manual Annotation of PathBlazer Objects with GO Terms To view edit or assign GO terms to database objects manually right click on the component reaction or pathway in the Explorer List Pane or displayed in a Discovery Pathway Graphics Pane Select lt object type gt Properties in the shortcut menu In the lt object type gt Properties dialog box that opens select the GO Annotations tab 157 Vector PathBlazer 2 0 User s Manual GO annotations display as a hierarchy on the tab if they have already been assigned to the object from which the Properties dialog box was opened Figure 7 5 Pathway Properties General Organisms Locations References Cross Links GO Annotations Expression Data aa Gene_Ontology R0 0003673 source DE lA cellular process GO0 0009987 SAU cell communication PO 0007154 Unique ID in DB oad T cell invasion GO 0030260 Evidence Type Organism Cancel Help Figure 7 5 Gene Annotations assigned to an object display on the GO Annotation tab of the Properties dialog box Add a gene ontology annotation by clic
129. e ibh Subset Description ee oao pe Figure 3 58 Appending search results to an existing subset You can also copy the selected objects by selecting Copy from the shortcut menu and then paste the copied objects to an existing subset in the Database Explorer by selecting Paste Add search results to a new subset by clicking Save the search results as a subset In the Create Subset dialog box enter a name and description for the subset and click Create Figure 3 59 All the search results listed are saved to the new subset Create Subset E EA Fl Pathways oof All Pathways El Demo Pathways Subset Name Pese Subset Description EEE rr pa Figure 3 59 Adding search results to a new subset Note Ifthe first search does not produce any results a Select Option dialog box opens at the conclu sion of the search allowing you to select another search option and re initiate the search 60 Working with Pathways Chapter 3 Search Database by GO Annotation Note This search finds objects in the database annotated with GO annotations you specify in the search conditions The search produces results only after objects in the database have been annotated with GO terms See ntroduction to Gene Ontologies on page 153 To search the database by GO Annotation you need to initiate the database search as described in Searching Objects in the Database and Creating Subsets on page 54 Select the object type in t
130. e Figure 3 56 Description and Datasource columns for Reactions and Components only also display values if they have been imported or entered for an object Search Components Create Subset aq EA Search Results tupe restriction enzyme d res BIND type Ill restriction enzyme d HP1371 BIND type ll restriction enzyme du mod BIND type I restriction enzyme d ECOS7IR BIND type IS restriction enzyme d bedi BIND type restriction enzyme M du ped BIND phosphatidylsenne decarbo du fad BIND acetyl coenzyme A acetyl du SPOBEC3G BIND APO lipoprotein B mANA E du IMPDH BIND Inosine 5 monophosphate d GnRS Glutaminyl tA MA erd A 110 items have been found Append selected items to subset Save the search results as a subset Herts Close Help Figure 3 56 Search with Single Condition results Multiple Condition Search The Name column in the left pane lists the query fields grouped by search values Figure 3 57 The right hand panel displays the batch search results with the number of search terms that were matched for each object found You can click on a column header to sort the table by a column s contents Drag the divider bars to widen or reduce the column widths View the properties of any object by first selecting it and then selecting Properties from the shortcut menu The Properties dialog box opens where you can review or change any of the object s properties Search P
131. e GO terms are removed and new terms are imported PathBlazer performs a search for GO annotations and those data base objects that it finds that no longer point to a valid Gene Ontology Term are listed in the GO Annotations Consistency Check dialog box that opens automatically only if there are terms being removed In such a case in the dialog box you must click on each object noted as having missing annotations and edit the annotations assigning new ones Working with Gene Ontology Annotations Importing Gene Ontology Annotations Gene Ontology Annotation is a dictionary which links GO categories to gene names names of pathways processes cell components etc These annotations can be applied during import to objects that are already stored in PathBlazer database Example The object Topoisomerase in PathBlazer has crosslinks to SwissProt P11387 Term GO 0003916 has a link SwissProt P11387 After the GO Annotations are imported Topoi somerase in PathBlazer will be annotated with GO term GO 0003916 Components reactions and pathways can have multiple GO annotations from each of three GO categories Process Component and Function Each GO term could be used in many anno tations in other words could be assigned to many objects 159 Vector PathBlazer 2 0 User s Manual 160 Notes Before importing the GO Annotations file you must first download and import the Gene Ontol ogy dictionary of terms See mporting Gene Ontology
132. e a template click Delete Click OK in the confirmation dialog box The template is removed from the list box 7 To close the Expression Import Template Manager dialog box click Close Importing a Template In Vector PathBlazer you can import expression import templates such as templates shared by colleagues Import the template by selecting Tools gt Manage Gene Expression Data gt Import Template Mapping Database Links Manually While creating templates automatically as described on page 166 is the ideal way to map data base to each other your file may not be compatible with that means of database object map ping If that is not possible you can map the database objects manually To associate gene names with pathway components manually use the following steps 1 Select Tools gt Manage Expression Data gt Import Expression Data A wizard opens to assist you in the steps to link gene names with components In the first screen the tab delimited file containing expression values is defined Select the expression data file by clicking the Browse button I Navigate to the file and click Open The Expression 171 Vector PathBlazer 2 0 User s Manual 172 Note Data File field displays the path to the file Figure 8 9 The Use Template field remains empty Click Next x Expression Data File C Documents and Settings jll NFORMAXINC My Dc EO Use Template Bact Cancel Help Figure 8 9 Define Sourc
133. e brikak Browse Load dictionaries Default o Classes EEE Browee Organisms organDict Browse Cancel Help Figure 4 14 TransPath Import dialog box for selecting the root folder and source files d Back 96 Importing Data Chapter 4 The other fields in this dialog box display the xml file names for the TransPath data These files are found in the root folder and you shouldn t have to locate them unless they are stored outside that folder Note Only files labeled in the import window by asterisks are absolutely required for successful import e Optional Check the Create Reverse Reactions for Bidirectional Reactions checkbox to execute that option e Optional Check the Load Dictionaries checkbox to use the custom dictionaries You will need to browse for the classDict and organDict files For more information about dictionaries see Custom Dictionaries on page 95 5 In the Merge Options dialog box select the options appropriate for merging the data See Merge Option Dialog Box on page 67 for more information Click Next to continue The data loads while a monitor displays allowing you to follow the import progress An import log summarizing import results displays when import has been successfully com pleted 6 Click Close Importing DIP Data DIP Database of Interacting Proteins is a database that documents experimentally determined protein protein interactions This database is inte
134. e components by selecting the Hide these Components checkbox and then selecting a component subset from the drop down list You can select all three of the checkboxes or none of the checkboxes depending on how you want to configure these parameters Show only connecting components by checking the Show Only Connecting Compo nents checkbox only connecting components will be displayed in the pathway you are building Find components or reactions that disrupt the pathway by checking the Calculate Criti cal Points checkbox This set of components and or reactions will constrict the pathway When they are deleted they will disrupt the pathway or increase its length These constricting ele ments of the pathway display in a color unique from the other colors in the pathway Limiting the Number of Steps Between Components 136 The Connection Length box in the lower left of the Build a Pathway dialog is for specifying the maximum number of steps that can be used to assemble a pathway The algorithm identifies the shortest possible pathway between two points based on the maximum number of steps entered If the number of steps of the shortest possible pathway is less than or equal to the maximum number of steps entered then the pathway is displayed If the shortest pathway is three steps and you have specified ten steps then all pathways with a length of three steps are shown If the shortest pathway has more steps than the specified limit a mes
135. e does not define an attribute correctly in one of the entries after the first entry the error in Figure D 2 is generated All entries that are defined correctly before the incorrect entry are imported into the database before the import halts In the following example a partial file is listed with the closing lt substance gt attribute crossed out to indicate it is missing which would cause the error shown in Figure D 2 The error message also shows the last entry that was successfully loaded into the database lt storage ID BIND Storage gt lt list_of_substances gt lt substance ID Prostaglandin E2 9 reductase gt lt list_of_origin_ accesses gt lt origin_access gt lt database gt KEGG lt database gt lt access gt EC 1 1 1 189 lt access gt lt item_URL gt http www genome ad jp dbget bin www_bget ec 1 1 1 189 lt item_URL gt lt extra_data gt KEGG Enzyme Link lt extra_data gt lt origin_access gt lt list_of_origin accesses gt substance lt list_of_substances gt 205 Vector PathBlazer 2 0 User s Manual Load From Stored XML Ioj x Read from ML file ERROR Cannot load data from ML File D PathBlazer Proprietary D atadatal sml Storage Statues Component subsh4 has been succestully loaded Clean up BREEN Figure D 2 Error generated when an attribute is defined incorrectly in the XML file Solution To determine where the source of the error is in the file look for any incorrectl
136. e for the reaction are taken from the reaction file 6 Names of organisms are taken from the genome file The result is a set of reactions in the database that each reference the appropriate components Although KEGG organizes the reactions listed in a rea file into pathway drawings Vector Path Blazer does not group these reactions into pathways Only reactions and components are cre ated from the source files However the referenced pathways are preserved in the reactions Table 4 3 Note Crosslinks from the KEGG have three distinct patterns Compounds db accession C11821 Enzymes db accession EC 1 7 3 3 Reactions db accession R00001 EC 3 6 1 10 In summary a db accession for a compound starts with letter C db accession for an enzyme starts with letter E and db accession for a reaction starts with letter R KEGG Compound File The Compound file is a collection of metabolic and other compounds including substrates prod ucts inhibitors of metabolic pathways drugs and xenobiotic chemicals Each of the chemical substances that appear in the Reaction and Enzyme files and the KEGG PATHWAY database is identified by an accession number and stored in this file Each Compound entry contains attribute fields for name chemical formula structural formula in a separate GIF file and a MOL file that cannot be imported into Vector PathBlazer metabolic pathways related enzymes related protein structures prosthetic groups and a CAS
137. e screen Selecting an expression data file Once a mapping between a gene list and a component list is completed and saved to the database you can use the mapping as a template and select it in the Use Template field Templates are described previously in this chapter The Map screen allows a mapping to be established between pathway components on the left and gene IDs names on the right The gene names contained in the expression data file automatically fill in the Expression Data list box in alphabetical order To select the pathway components click the Browse button under Pathway Components and select the appro priate subset In the following example glycolysis components are organized in a subset in the database and display in alphabetical order in the Pathway Components list box Figure 8 10 Pathway Components 1 3 Bisphosphoglycerate 2 Phosphoglycerate 3 phosphoglycerate ADP Component Aldolase ATP Dihydroxyacetone phosphat Enolase Fructose 1 6 bisphosphate Fructose 6 phosphate Glucose I Link Orphan Genes Relink All Genes Using DB Links Using Names and Synonyms Using DB Links Using Names and Synonyms lt Back Next gt Cancel Help Figure 8 10 Map screen for associating components with gene names IDs Link components that is gene products from the Pathway Components list box to gene names IDs in the Expression Data list box b
138. eactions are listed in the left panel Figure 3 45 Save Reaction Components Reaction 1 of 1 3 EA Name Direct Role Stoic Trans d Reaction gura rent do Components 1 3 Bisphophogly Input Normal 1 1 000 a l Glyceraldehyde d Output Normal 1 1 000 e Properties MADH Input Normal 1 1 000 Constants NAD Output Normal 1 1 000 Conditions Glpceraldehyde 3 Input MOS 1 000 Organisms Locations Cross Links A Pathways Complete Properties Cancel Help Figure 3 45 In the Save dialog box for saving reactions not going through a pathway only components and prop erties of the selected reaction display The Name column displays each component in the reaction and the remaining columns display information about the connector to which the component is associated in the reaction Proceed through the Wizard as described in the previous section starting with step 6 on page 48 entering the information appropriate to the reaction you are saving Use the Back and Next buttons for advancing through the screens in sequence 50 Working with Pathways Chapter 3 Note If you try to change a component that is used in another reaction that is not currently selected a message displays that the component is shared with a non selected reaction and cannot be changed at this time If no reactions are selected the menu command Save Selected Reactions saves all reactions in the Graph
139. eaded arrow can be dragged to the left or right FSS ector PathBlazer 2 Glycolysis Pathway ia EEE Ioj xj Menu Bar ile Edit View Tools Layout Window Help e BEE Ga E Toolbar k x E b E E ES e X La Ss Expression Data Sets None gt Expression Runs E Ib oaa TRI OTS ff 7B zZz Ul A 8 a mw mw amp GEO ES Glycolysis Pathway Discovery unrestricted view Database E loj x Physical E EEAO Divider aie Bar ADP Glucose 6 phosphate Pathway Glucose 6 phosphate 9 e e i isomerase Viewing Area Fructose 6 phosphate ATP Divider Bar ZL PathBlazer Database C 3 Components All Pathways Subset H Reactions Database SZ DU Pathways ZU Experiments Collection of Pathways us Explorer Status Bar Figure 3 2 Elements of Pathway Viewer 11 Vector PathBlazer 2 0 User s Manual Pathway Viewing Area The Pathway Viewing Area in the middle of PathBlazer Viewer is for building viewing drawing editing and finding elements in a specified pathway When you first open PathBlazer Viewer the Pathway Viewing Area is initially not available until you select a component reaction or pathway for display Experiments display only in conjunction with an open pathway The Pathway Viewing Area is made up of a Graphics toolbar at the top a Palette window on the left and a Graphics window on the right Figure 3 3 The Graphics window initially has two tabs
140. earch This opens the PathBlazer application and the search is transferred to the PathBlazer search engine It includes prompts for further defining the scope of the search For more information see Searching Objects in the Database and Creating Subsets on page 54 Search results display in the same format as do object searches launched from PathBlazer For more information see Search Results on page 58 For more information about working in Vector Xpression refer to the Vector Xpression 3 0 User s Manual and the Vector Expression 3 1 User s Manual Addendum Displaying Expression Data on Pathways 178 Once components have been mapped to gene names IDs and colors have been assigned to expression value ranges you can display expression values on pathway components To do so you must associate expression experiments with pathways Use one of the following methods to initiate the display e Select an Experiment subset in the Database Explorer List Pane Right click on the Experiment and select Associate With In the dialog box that opens locate and check one or more pathways you want to associate with the Experiment Click Select The association are saved to the database e Open a pathway Click on an Experiment in the Database Explorer List Pane and drag it onto the pathway in the Graphics Window e Select an expression data set from the Expression Data Set drop down list in the Graphics toolbar Figure 8 17 If no data sets are as
141. eating an Template Automatically on page 166 e mporting Expression Data with a Template on page 168 e Creating a Tab Delimited Data File of Expression Values on page 174 e Displaying Expression Data on Pathways on page 178 e Modifying Display Colors for Expression Value Ranges on page 181 Introduction to Expression Data Import and Display In Vector PathBlazer gene expression data can be displayed in the context of pathway topology by linking gene names to gene products that is pathway components To do this expression data is imported into PathBlazer and links are made between genes expression values and component names Expression data can be forwarded to PathBlazer 2 0 directly from Vector Xpression 3 1 or intermediate tab delimited text files can be created from other software then imported Displaying expression data on pathway components in the Graphics window is a three step pro cess e First a data file that contains expression values is created if Vector Xpression is not used e Second expression data is linked to pathway components via gene names e Finally display colors are assigned to expression value ranges 165 Vector PathBlazer 2 0 User s Manual Once the preparatory steps have been completed expression values can be displayed on a pathway that has components in common with the genes in the expression data Interaction Between Vector PathBlazer 2 0 and Vector Xpression 3 1 One of the advantages of work
142. ected then all components connectors and reaction node connected to A and including A are replaced with a sign D D D ood Sun alt o EE io GN da g Figure 3 13 Hiding children e Hide Parents hides the forming elements of the selected element at the selected level e Hide Neighbors hides all elements at the selected level e One Level means the elements directly associated with the selected element e N Levels opens a dialog box to enter the number of levels to be hidden that are associ ated with the selected element e All Levels means all associated levels of the selected element are hidden Customizing Graphical Properties In the Graphics window you can customize how individual objects display in terms of shape size font shading etc Alternatively you can apply different graphical layout formats to all like objects in a pathway as a whole using the customize universally feature You can also custom ize display for all objects with a specified gene ontology Object and Graph Display Properties The graphical properties of objects and graphs are those that display in the Graphics window such as the size shape and color of a component the font color of a label and the position of an object in the image as a whole These properties can be customized for each object View and modify an object s graphical properties by selecting the object in the Graphics window and selecting View gt Object Properties or Object
143. ed by clicking the Browse button and locating the mdb data Working with Gene Expression Data Chapter 8 base Figure 8 1 The default location is in the C My Documents My PathBlazer Data directory Create PathBlazer template E X Select PathBlazer database C Documents and Setting INFOR MASINES My Documents My FP D Browse Select template file C Documents and Setting INFOR MASINES My Documents My Pathe Browse Back Cancel Help Figure amp 1 Create Template wizard first screen for selecting the PathBlazer and expression data files to be mapped to each other In the Select Template File field choose the expression data file by clicking the Browse button and locating the txt file Click Next In the second screen of the Wizard the PathBlazer database to which components in PathBlazer are linked displays Figure 8 2 Create PathBlazer template e xX PathBlazer database FORMASINC My DocumentssMy PathBlazer Data PathBlazersPathBlazer demo db rd Mapping options Delimiters ZZ Use Gene Name Use Altemative Name Use Foreign Key Use Delimiters f Tab Space PathBlazer crosslink database name EIND DI Eomma Expression UDF name Other Columne T Template name Hew Template DI Ga f Semicolon Za r lt Back Cancel Help Figure 8 2 Second screen of Create Template wizard to select mapping options In the
144. ed from pre built subsets for starting and ending the pathway as well as limiting the pathway For more information about creating subsets see Organizing Pathway Data on page 33 and Searching Objects in the Database and Creating Subsets on page 54 Automatically Assembling Pathways Chapter 6 The Path box in the upper left of the Build a Pathway dialog box is for specifying start end and through components or pathways when building a pathway Specifying start end and through components or pathways is optional When Vector PathBlazer is given the name of two compo nents or pathways it generates potential pathways from one component or pathway to the other If only the start component is specified and a number of steps is defined see below the program generates all pathways from the start component or pathway up to n number of steps Identify the start component or pathway by selecting the Build Pathway from Compo nent or the Build Pathway from Pathway checkbox Selecting a start component or pathway is optional You can either browse for the starting component or pathway by clicking the Browse button and selecting a component or pathway from one of the component subsets in the data base or you can enter the name of the component or pathway in the text field Synonyms can also be entered in the text field You can build a pathway in either the forward or reverse direc tion from that component or pathway Parameters for direction are described
145. ed with blue han dles Figure 3 49 EA E NADF Za H N N N c02 Figure 3 49 Found component is centered and selected in the Graphics window Searching Objects in the Database and Creating Subsets 54 An extended search can be performed on all pathways reactions and components in the data base as well as on annotations that have been added to any objects Subsets can also be cre ated directly from the search results To search the database and or create subsets use the following steps 1 Select Tools gt Search Database or gt Create Subset Both commands open the Search Create Subset wizard Figure 3 50 You can also click the Search button C in the Explorer toolbar In the first screen select the radio button corresponding to the type of object you want to search for and click Next Search Create Subset E Ee E Select the type of them you wish to search the database far f Pathway Reaction I Component Figure 3 50 Search Create Subset wizard selecting a type of object to search for 2 The next screen contains options for configuring one or more search conditions Figure oo 1 Click Add Single Condition to specify a single condition for the search You can click this button more than one time to add more than one individual condition To continue with this option proceed with step 3 then move directly to step 6 on page 57 Click Add Multiple Condition to specify a s
146. els added to reaction nodes 132 CHAPTER AUTOMATICALLY ASSEMBLING PATHWAYS This chapter describes how to use Vector PathBlazer to suggest novel pathways and protein protein interaction networks from known components and reactions Topics in this chapter include e ntroduction on this page e Pathway Assembly Parameters on page 134 e Assembling Metabolic Versus Discovery Pathways on page 138 e Adding Stepwise Reactions to Pathways on page 138 e Building Pathways by Selecting Reactions in the Database Explorer on page 139 e Examples of Automatically Assembling Pathways on page 139 Introduction The previous chapters described how known pathways are represented in Vector PathBlazer and how to import draw and manage known pathways This chapter describes how to use Vec tor PathBlazer to perform its most important function using known pathway and reaction data to build novel pathways Many molecules such as ligands and receptors are known to participate in many pathways and may effect different reactions under normal and disease states Suppose you are studying the EGF EGF receptor interaction in the context of malignant melanoma but you do not know any of the downstream interactions You want to know based on the data sets you have loaded into your database KEGG BIND DIP TransPath BioCyc PPI and or proprietary what other mole cules are known to interact with this complex To do this you build queries in which you spec
147. ence_level BioNet gt lt ATTLIST interaction ID ID REQUIRED gt lt list_of_conditions gt lt ELEMENT list_of_ conditions condition gt lt ELEMENT condition CDATA REQUIRED gt lt IATTLIST condition type CDATA REQUIRED gt lt list_of_diseases gt lt ELEMENT list_of_diseases disease gt lt ELEMENT disease database access item _URL gt lt ATTLIST disease name CDATA REQUIRED gt lt ELEMENT reversible Yes No gt lt ELEMENT effect HPCDATA gt lt ELEMENT confidence_level HPCDATA gt lt ELEMENT reaction list_of_origin _accesses creator create_date update_date 194 list_of_hyperlinks synonyms type group _name list_of_subcomponents definition of locations list_of_ pathways names list_of_annotations list_of_reference_accesses comments list_of_conditions list_of_diseases reversible effect confidence_level BioNet list_of_formulas list_of_constants gt lt ATTLIST reaction ID ID FREQUIRED gt lt list_of_constants lt ELEMENT list_of_constants constant gt lt ELEMENT constant CDATA REQUIRED gt lt ATTLIST constant type CDATA REQUIRED gt lt ELEMENT pathway list_of_origin_accesses creator create_date update_date list_of_hyperlinks synonyms type
148. enolpyruvate gt lt agent gt lt agent ID H20 gt lt role gt product lt role gt lt substance ref H20 gt lt agent gt lt agent ID Phosphopyruvate hydratase gt 103 Vector PathBlazer 2 0 User s Manual lt role gt catalyzing agent lt role gt lt substance ref Phosphopyruvate hydratase gt lt agent gt lt list_of_agents gt lt list_of_actions gt lt action ID Gly 1 gt lt reaction ref Gly 1 gt lt action gt lt list_of_actions gt lt list_of_arcs gt lt conf_arc from 3 ADP 2 phosphoglycerate to Gly 1 TransitionProbability 0 gt lt bidirect gt No lt bidirect gt lt type gt ordinary lt type gt lt weight gt 1 lt weight gt lt conf_arc gt lt conf_arc from Gly 1 to Phosphoenolpyruvate TransitionProbability 0 gt lt bidirect gt No lt bidirect gt lt type gt ordinary lt type gt lt weight gt 1 lt weight gt lt conf_arc gt lt list_of_arcs gt lt BioNet gt lt reaction gt Defining Pathways The third part of the file contains a list of pathways Each pathway contains a list of components and reactions For each pathway described between the lt BioNet ID gt attribute a pathway object is created in the database with the unique ID that is included in that attribute The lt list_of_agents gt attribute describes each component in the pathway The name of the actual component is determined from the lt substance ref gt element who
149. ent in Vector Xpression From a specific Experiment object selected in PathBlazer 2 0 you can open the corresponding Experiment in Vector Xpression if the Experiment originated in Vector Xpression To do so complete the following steps 1 2 In the PathBlazer Database Explorer select an Experiment in an Experiments folder Right click on the Experiment and select Open in Vector Xpression from the shortcut menu Click Open Vector Xpression opens with the Experiment displayed in an Experiment Viewer Sending Expression Data to PathBlazer From Vector Xpression 3 1 you can send expression data directly to Vector PathBlazer 2 0 without creating an intermediate file 1 9 In the Vector Xpression Database Explorer select Expression Genes from the Tables drop down list and then select the gene s that you want to map or Open an Expression Runs Viewer Runs Project Viewer or Experiment Viewer displaying data with genes that you want to map Select the gene s that you want to map Select Tools gt Send Expression Data to PathBlazer The Save Experiment s in PathBlazer database dialog box that opens displays the Experi ment you have selected In the Use Template field select the template where the expres sion data is mapped In the PathBlazer database field select the database where the Experiment is to be stored Figure 8 16 Save Experiments to PathBlazer database EA Experiments Speed tutorial
150. ent topic Click gt gt to go to the next topic in a sequence Click lt lt to go to the previous topic in a sequence When a See Also button is present in a topic click the button to display a list of related topics that you can go directly to Click the green colored text to jump to a linked topic Contacting Technical Support USA Phone 240 379 4240 800 357 3114 Toll free U S E mail techsupport informaxinc com Europe Phone 44 186 5784591 Vector PathBlazer 2 0 User s Manual For online technical support send your questions to techsupporteurope informaxinc com Conventions Used in this Manual The following table lists conventions that are used to differentiate between regular text and menu commands keyboard keys toolbar buttons dialog box options and text that you type Table 7 7 Convention Description Bold amp Capitalized Command Indicates a menu command Indicates sequential menu commands Bold amp Capitalized command gt Bold amp Capitalized command Example Select Edit gt Copy TEXT IN SMALL CAPS Keyboard key that you press Example Press ENTER TEXT IN SMALL CAPS Keyboard keys that you press concurrently TEXT IN SMALL CAPS Example Press SHIFT CTRL and then release both TEXT IN SMALL CAPS Keyboard keys that you press in sequence FOLLOWED BY Example Press ENTER then TAB to commit the change TEXT IN SMALL CAPS A button that you click Example Click the Delete button
151. ents and reac tions by selecting Tools gt Filtering Highlighting gt New Filtering Highlighting Schema This opens a Filtering Highlighting dialog box with at least Default Color listed Figure 3 16 Filtering Highlighting E EA i i Add Component Default Color Edit Delete Figure 3 16 The Filtering Highlighting dialog box allows you to customize display for objects universally To specify a color for a class of component click Add Component In the Add Condition dialog box select the Condition Type from the drop down menu Then select the Component Class from the drop down menu When you choose some of the component class options additional suboptions display Figure 3 17 Add Condition E x Condition Type Component Class Component class Protein Protein subclass Enzyme EC Number Genenc Name Display Option go Choose Color add Cancel Help f Hide Figure 3 17 The Add Condition dialog box adds suboptions for some of the Condition Type and Component Class selections 21 Vector PathBlazer 2 0 User s Manual 22 Note Click the Choose Color button at the bottom of the box In the color box that opens select the color for the specified component display An alternative is to select the Hide radio button to hide all of the specified components When you click the Hide button a second time hidden objects display As an example say that you want all enzymes in the
152. er 4 Use the following steps to import PPI data into the Vector PathBlazer database 1 d Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 From an open PathBlazer window select File gt Import The PathBlazer Import tool opens displaying the various import options Figure 4 17 PathBlazer Import E xj Select import module Trans lronort TransPath data Descriptions bo data from UserPF file lt Back Cancel Help Figure 4 17 User PPI file selected for import In Screen 2 of the Import Wizard select the User PPI file for import by clicking the Browse button Locate the corresponding file in the Open dialog box and click Open The complete path to the file displays in the Select source file field Figure 4 18 Click Next to continue E PathBlazer Import User s datasource name UserPP Organism User s PPI file eau zer PPI Browse lt Back Cancel Help Figure 4 18 PPI Import dialog box for selecting source file In the Merge Options dialog box select the options appropriate for merging the data See Merge Option Dialog Box on page 67 for more information Click Next to continue The data loads while a monitor displays allowing you to follow the import process An import log summarizing import results displays when the import has been successfully com plete To stop the import click Cancel Click Close
153. er in xml format The Database Explorer window behaves similarly to a Windows based Explorer and is made up of the Explorer toolbar the Contents Pane on the left and the List Pane on the right Figure 3 4 A main folder displays under the Pathway Database icon for the four main data types Selecting a folder or container in the Contents Pane displays its contents in the List Pane A divider bar separates the Contents and List Panes and can be dragged to the left or right to change the size of these panes ie ector PathBlazer 2 i Ioj x File Edit view Tools Layout Window Help Explorer Toolbar Van dek EE 2 a l Expression Data Sets No ne Expression Runs L Contents Pane x E de gt EO Fe e zes fl A zal 9 b Izo g ES A lezez IES e ed PathBlazer Database C List Pane Ed i 4b L C64618 UserPPI PPI role Trapped protein ls 12 1 T bi filter peo L C64641 UserPPI PPI role Trapped protein i 12 1 SO intersection jbh ap L C64647 UserPPI PPI role Trapped protein i 12 1 B Gi new jbh pL Ca channel active INMX 12 2 Divider Bar pL Cat channel inactive INMX 12 2 SL Components pl C64601 fal All Components ga ceq613 all cL CL molecules W Small Molecules 4b L CACM_YEAST GO union jbh db L CAP_YEAST Reactions 4 L carnitine Pathways l carnitine dehydratase Si Al Pathways q L CARNITINYL COA 4 Demo Pathway 4L CASR_HUMAN UserPPI UserPPI
154. eral URL displays in the shortcut menu of a selected object in the Graphics win dow The following figure Figure 3 47 shows an object with four crosslinks defined the first three are URLs to various databases for example www expasy org and the fourth is the dis play name to a protein in the Vector NTI database for example Interleukin 8 Receptor B To open any crosslink click on it in the shortcut menu If the link is a URL the default browser opens to the specified page If the link is to Vector NTI the viewer opens in the appropriate Vec tor NTI program EES vector PathBlazer 2 Reaction INTERACT 4167 B 8 x File Edit Yiew Tools Layout Window E BE E gt ei EE KO x Expression Data Sets None D Expression Runs Roars xo vee of ABZ Ul A O 8 ww wo ZZ Reaction INTERACT 4167 Discovery unrestricted view Database a e Oj xj DNA RNA ab e Enzyme Protein o o o D DEEI m a TERN e Copy Ctrl C Undetined Append Selected Components to Subset ee Save Selected Components as Subset H20 Gide Selected Reactions to Subset Save Selected Reactions Subset Normal Hide d Create Label Interaction Object Properties gies Component Properties Catalysis Change Component Display Name alysi e Add Reaction TE Activation 4 supert PTE e BIND Search gt Zt 3 BIND Protein Link E gt A BSL d a x fl Small Molec 4 b
155. erwise only the Visible Window Only checkbox is available 63 Vector PathBlazer 2 0 User s Manual 64 Save 45 Image Image Content Visible Window Only Selected Objects Only Image Characteristics Image Quality 0 100 75 Curent Zoom Level bk Preserve Aspect Ratio GZ Actual Size Mik i146 ZI Other Height ES Minimum File Size unknown Figure 3 63 Save as Image dialog box 5 In the Image Characteristics field set the image quality by dragging the pointer between Low and High 6 Inthe Size field select the size you want the image to be saved in 7 Click OK The image is saved with the properties you selected in the specified location You can also copy any selected elements in the Graphics window to the clipboard and then paste them into a word processing program as a jpeg image only To copy an image use the SHFT key or the CTRL key to multiple select elements or use the Select commands in the Edit menu and then select Edit gt Copy to clipboard to copy the selected elements to the clipboard CHAPTER IMPORTING DATA This chapter describes how to import public and proprietary data into Vector PathBlazer Topics in this chapter include Introduction to Importing Data on this page About Vector PathBlazer Data Import on page 66 Importing KEGG Data on page 72 Importing BIND Data on page 80 Importing BioCyc Data on page 85 Importing TransPath Data on page 93 Importing DIP Data on p
156. es EE m e for drawing HOR connectors Interaction Catalysis Activation Inhibitior Figure 5 1 Palette of drawing tools Component Shapes and Connector Lines Shapes and lines in the Palette window can be used to represent any kind of molecule or inter action for example protein DNA etc and are labeled to suggest a template for their use For example the oval is labeled Enzyme to suggest that each time you draw an enzyme you use an oval Components and connectors are automatically assigned the type suggested by their labels However once a shape is created assigned a name and saved to the database you can change the shape in the Graphics window without changing the type associated with the shape You can permanently change the type by modifying it in the object s annotations For more information about annotating objects see Annotating Pathways Components Experi ments Reactions and Connectors on page 37 Available shapes and their suggested uses are shown in the following table Table 5 7 Physical factor Example heat light etc Table 5 1 Shapes in the Palette window Drawing Pathways Chapter 5 i rectangle Protein Unidentified molecule Table 5 1 Shapes in the Palette window Continued Available connectors and their suggested uses are shown in the following table Table 5 2 Unidirectional reaction that can be used to indicate a left to right or a right to left reaction direction Note To create a r
157. esize the image by using one of the following methods e Select View gt Overview Navigation Window or click the Overview button on the Graphics toolbar to open a second window called the Overview window that is indepen dent of the Graphics window Figure 3 12 The Overview window allows you to view the entire pathway while you zoom in on details of the pathway in the Graphics window The Overview window contains a shaded rectangle or boundary which can be resized by dragging the handles on any of the corners and can be dragged around the window As 17 Vector PathBlazer 2 0 User s Manual the boundary is resized and dragged in the Overview window the contents of the bound ary are resized and positioned in the center of the Graphics window EES vector PathBlazer 2 Glycolysis Pathway E Oj x File Edit view Tools Layout Window Help KE e gt led EE ES KO KA OA Expression Data Sets None Expression Runs jz AQ Rio ele r J J Z ula gt F i h A 33 Glycolysis Pathway Discovery unrestricted view Database Physical lt P gt Hexokinase DNA RNA Glucose 6 phosphate Glucose 6 phosphate isomerase Undefined D Fructose 6 phosphate H20 ATP E Figure 3 12 Overview window Note To tile the Overview window with the Palette window double click on the title bar of the Overview window To return it to an independent window double click on its title bar
158. et and press ENTER Create a subset with specific contents by selecting one or more objects in the List Pane and then selecting Create Subset from the shortcut menu Select a list of consecutive objects by selecting the first object pressing the SHFT key and selecting the last object Select non con secutive objects by pressing the CTRL key and selecting the objects In the Create Subset dia log box select the folder to contain the new subset enter a name and description and click Create Figure 3 32 The subset is created in the List Pane and contains the selected objects You can create a new subset containing all of the items in two or more existing subsets of like object types union or the items common to two or more existing subsets of like object types intersection e To create a new subset that contains all the items of two or more existing subsets high light at least one subset in the List Pane then click the Union button E on the Explorer toolbar Check the two subsets whose contents you want to combine Click the Results Subset button and in the dialog box that opens enter the Name of the new repository subset Click OK e To create a new subset containing items common to two or more existing groups high light at least one subset in the List Pane then click the Intersection button JEU on the Explorer toolbar Check the two subsets whose common contents you want to combine in the intersected subset Click the Re
159. et of multiple conditions for the search You can specify only one set of multiple conditions for a search One multiple condi tion can be combined with several single search conditions however To continue with this option proceed with step 5 on page 57 Working with Pathways Chapter 3 Search Pathways Create Subset E x Search Conditions Add Single Condition Add Multiple Condition Edit Delete Logical Condition Association f D ZI And Custom Search In Subset J Pathways Eo All Pathways Demo Pathways Gi Metabolic Pathways a Gi Signaling Pathways TTU i la Back Close Help Figure 3 51 Search Create Subset wizard configuring a query 3 In the Add Single Condition dialog box select a field from the Condition Type drop down list Figure 3 52 The list displays the annotation options for each type of object Options depend on which kind of object you are searching for The field that is selected in the Condition Type determines the names of additional fields in this dialog box Add Condition oOo E Tenda Tie Pathway Name i ei P at h Wha N ame Hame Reaction Hame Component Name Description D atasource Confidence Figure 3 52 Add Condition dialog box 4 Enter an appropriate value in the additional fields or select from a drop down list of options For a list of annotations see Annotating Pathways Components Experiments Reactions and Connectors on
160. et s that have a component in common with the selected component are searched and presented in a list To add a reaction using this method use the following steps 1 Select a component in the Graphics window and then select Add reaction from the shortcut menu When adding a reaction by this method components are only searched by primary name and not by synonym If the component you have selected matches any other components by synonym those reactions are not displayed in the returned list 125 Vector PathBlazer 2 0 User s Manual 2 Inthe Add Reactions dialog box select the direction in which you want the selected com ponent to participate in any matching reactions Figure 5 21 Select from the options in the drop down list in the Role of field Input PPI Output or Catalyzing agent Consider the options in the context of the following reaction glucose ATP hexokinase gt glucose 6 phosphate ADP Input PPI means any reaction that includes the selected component as either an input to a reaction or part of a protein protein interaction since these types of interac tions are non directional If glucose were the selected component the reaction above would be returned since glucose is an input to the reaction Output means any reaction that includes the selected component as an output of a reaction If glucose 6 phosphate were the selected component the reaction above would be returned since glucose 6 phosphate is an o
161. eversible reaction two separate and opposite reactions are created using this con nector e Protein protein interaction Note A straight line automatically confers protein protein interaction on a reaction and only displays when drawing in Discovery Unrestricted View 4 Catalysis reaction Note This line only displays when drawing in Dis covery Unrestricted View e au Activating reaction Table 5 2 Connectors in the Palette window Commonly Used Molecules In addition to the shapes that can be used to represent any kind of molecule a list of commonly used molecules is provided by the drop down menu next to the symbol in the Palette window A number of small molecules such as H20 and ATP have already been created as components in the default database that is installed when Vector PathBlazer is installed and can be further annotated to suit your needs Each small molecule references the corresponding component in the database by primary name The drop down list includes the following small molecules e H O e Oxygen e NAD e Orthophosphate e NADH e CO e NADP e KI e NADPH e FAD 111 Vector PathBlazer 2 0 User s Manual Note Note e ATP e FADH e ADP When a new database is created the list of small molecules above is automatically created in the new database Add a component to the list by selecting Tools gt Options and clicking the Set Palette Pull Down Molecules tab in the Options dial
162. ew Fil tering Highlighting Schema This opens a Filtering Highlighting dialog box with Default Color listed To customize gene ontology display click the Add Component button Before you can display gene ontologies you must import the gene ontology files See ntroduc tion to Gene Ontologies on page 153 Working with Pathways Chapter 3 In the Add Condition dialog box select Component GO Annotation from the Condition Type drop down menu This opens an Add Condition dialog box specific to Gene Ontologies Add Condition E E Condition Type Component GO Annotation D Find GO Term Select GO Term ERSE Gene Ontology G0 0003673 E rr SEO molecular function ISU 00036 4 SE biological process GO 00087 BOI Ft behavior GO 000761 0 biological_ process unknown GO 00000 cellular process GO 0009987 development GO 0007275 obsolete biological process GO 00083 physiological processes ISU DUD 7582 viral life cycle GO 001 6032 cellular component G0 00055 5 ba bed Md Ubi Urd Led Ube gt l Evidence Type Any Traceable Author Statement best E Display Option f Choose Color sa Cancel Help Hide Figure 3 19 Add Condition dialog box for Gene Ontologies Select any GO term that you would like to set as a condition or search for a GO term by entering the term in the Find GO Term text box Click the Find button Suboptions that allow you to choose display color or show hide the a
163. example in Reaction 1 the stoichiometric constant can be set to Working with Pathways Chapter 3 two since two molecules of Mol A are required to form A2 For more information about annotat ing connectors with stoichiometric constants see Annotation Fields for Connectors on page 44 Rxn 1 Bra MOA m AZ ed 3 Tre Ad AS Figure 3 11 Dimer trimer and tetramer formation Navigating Objects in the Graphics Window You can move select and resize individual objects or all objects at the same time in the Graph ics window Use the following operations to move and resize objects Rearrange objects by selecting an object that is a component connector or reaction node in the Graphics window and selecting Tools gt Pointer Select or the Arrow icon b on the Graphics toolbar Select a component connector reaction node and drag it to a new place in the window When you select a connector and drag it a bend is introduced Lr ee L When you select a reaction node and drag it all of the components and con nectors that are linked to it move with it When you select a component and drag it any connec tors that are linked to it move with it Pan the entire image by selecting View gt Pan or the Hand icon am on the Graphics tool bar The cursor changes to a hand As you drag the hand with the mouse in the Graphics win dow the entire image in the Graphics window moves with it as one image R
164. f interactions gt lt placed into list_of_interactions gt lt ELEMENT interaction_ref interaction reaction pathway reaction gt lt ATTLIST interaction_ref ref IDREF REQUIRED gt lt Description of Arc gt lt ELEMENT list_of_arcs conf_arc gt lt IDREF references to agents actions gt lt placed into list_of_agents list_of_actions respectively gt lt ELEMENT conf _arc bidirect type weight conf_level expression gt lt ATTLIST conf_arc from IDREF REQUIRED to IDREF REQUIRED gt lt ELEMENT bidirect Yes No gt lt ELEMENT type ordinary enabling disabling gt lt ELEMENT weight HPCDATA gt lt ELEMENT conf_level HPCDATA gt lt expression should be conformable to Perl grammar gt lt ELEMENT expression HPCDATA gt 197 Vector PathBlazer 2 0 User s Manual 198 General KEGG Description URL APPENDIX REFERENCES This appendix contains a list of references to locations and citations where you can obtain more information about key concepts in Vector PathBlazer Fell DA Understanding the Control of Metabolism Portland Press 1996 Girault C and Valk R Petri Nets for Systems Engineering Springer Verlag 2002 First Edition Kanehisa M Post genome Informatics Oxford University Press 2000 Kitano H Foundations of Systems Biology The MIT Press 2001 Peterson JL Petri Net Theory and t
165. for the type of object Example gt Tight width can resize vertically only Example gt Tight height can resize horizontally only Example gt Tight fit preserve aspect cannot resize If object has been resized the size is retained Example gt Preserve aspect ratio can scale If object has been resized the shape is retained Example gt Change the Width and the Height by selecting the object in the Graphics window and dragging it by any of the handles The values for width and height in the Properties box adjust accordingly Change the position of the object from the center of the Graphics window by selecting it and dragging it The values of X Center and Y Center adjust accordingly You can also enter values in these fields in the Properties box and the object moves to the corre sponding position in the Graphics window Working with Pathways Chapter 3 Customize an individual object s font and color from the Graphics toolbar by selecting an object such as a component and then changing the font s style size and color by making selections from the font buttons and drop down lists in the Graphics toolbar Figure 3 15 You can also change the fill color of a shape by selecting a color from the drop down list next to the bucket icon E Comic Sans MS Ahe BiZ ul A D Figure 3 15 Changing object fonts and colors from the Graphics toolbar Customize universal color schemes and display for selected compon
166. from a gene expression data file and a set of component names Text View Tab in the Graphics window in which a pathway and its associated data is viewed in text format as opposed to graphical format A Adding Alternate Views in Graphics window 29 annotations to objects 37 components to Graphics window 113 118 121 component to saved reaction 128 folders to Database Explorer 34 labels to Graphics window 131 molecules to commonly used molecules list 111 reactions to Graphics window 122 125 reaction to Graphics window 125 reverse reactions 35 search results to subsets 59 subsets to Database Explorer 34 Alternate View copying 31 creating 30 deleting 31 description 29 Annotating objects description 37 objects as a batch 38 objects with GO annotations 157 Annotations component 39 connectors 44 description 37 pathway 39 reaction 39 Annotations See Gene Ontology 153 Attribute See Annotations 37 B Background color in Graphics window 20 Batch annotation 38 BIND description 80 import instructions 84 import logic 81 83 source files 81 BioCyc Component files 87 description 85 import instructions 92 import logic 86 Pathways file 90 Reaction files 89 source files 86 Border color in Graphics window 20 Browsing in Database Explorer 31 Building pathway Index adding a stepwise reaction 147 default colors 138 from starting component 139 from starting pathway to ending component 143 from starting to ending
167. g a from component a to component and a through component Starting component is Glucose ending component is Pyruvate through component is Fructose 6 phosphate number of pathway steps is ten Same as previous example 1 Select Tools gt Build a Pathway gt Build Discovery Pathway 2 Inthe Build a Pathway dialog box select the Build Pathway from Component checkbox and enter Glucose as the starting component 3 Select the Build Pathway to Component checkbox and enter Pyruvate as the ending component 4 Select the Build Pathway through Component checkbox and enter Fructose 6 phos phate In the Include Reactions from Subset field select the Glycolysis reaction subset Set Max number of steps to 10 Set Extra steps to 0 Select Ignore Paths through these Components and select the Small Molecules subset Select Don t Pool Components in Subset and select the Small Molecules subset Ee GE ERE a d 0 Set Direction to Forward 145 Vector PathBlazer 2 0 User s Manual 11 Set Interaction Generality to Unlimited The Build a Pathway dialog box should look simi lar to that in Figure 6 9 Build a Pathway E 3 i E x Fath Build Pathway la from Component from Pathway glucose Browse Build Pathway kd to Component to Pathway pyruvate Browse M Build Pathway through Component fructose phosphate Browse Include Reactions from Subsets Component Subsets le
168. g ligand ligand doc The 3 letter abbrevia tions are defined by links made to the Genome file Disease Link information to disease descrip Component CrossLinks tions in OMIM Online Mendelian A pre defined URL that matches the Inheritance in Man OMIM database is automatically defined Pre defined URLs are listed in Pre Defined URLs on page 107 Motifs Link information to motif definitions Component CrossLinks in the Prosite database A pre defined URL that matches the Prosite database is automatically defined Pre defined URLs are listed in Pre Defined URLs on page 107 Table 4 3 Imported attribute fields from the Enzyme file 76 Field Name Structures DBLinks Description Link information to 3 D protein structures in PDB Protein Data Bank Link information to other databases including IUBMB Enzyme Nomenclature ENZYME Nomenclature database at Swiss Institute of Bioinformatics WIT What Is There Interactive Metabolic Reconstruction on the Importing Data Chapter 4 Component Annotation in Vector PathBlazer Component CrossLinks A pre defined URL that matches the PDB database is automatically defined Pre defined URLs are listed in Pre Defined URLs on page 107 Component CrossLinks A crosslink of type URL is automatically created for all KEGG enzymes A link is made to the URL_http www genome ad jp dbget bin www_bget enzyme lt EC Number gt where lt EC Number g
169. ge or add any of the attributes On each tab select the appropriate radio button Don t Apply Append or Replace an existing annotation Note that any changes you make will be assigned to ALL of the selected subset s contents Click OK to apply the changes Subset Content Properties Organism Location Description Tyee Eee Name E i Dont apply i Append Replace Cancel Help Figure 3 37 Subset Content Properties dialog for reviewing or applying batch annotations Annotation Fields for Components Reactions and Pathways Many of the annotation fields for pathways components and reactions are the same For exam ple each of these objects can have a location associated with them Table 3 5 lists the annota tion fields values and descriptions for pathways components and reactions first by the screen or tab in which they are found Annotation fields for connectors are listed later in this section Tab Description Gid Sa EEEn Field Value s Reaction R Component C General Name Primary name of the object Component Example Glucose String Datasource Origin of the object Example KEGG String Note If an entry is imported from two data sources for example KEGG and DIP the data source displays both sources For exam ple if a component was first imported from KEGG and then from DIP this field displays KEGG DIP Disease Disease or condition associated with the object
170. gin_ chem gt lt BIND object origin gt lt BIND object_origin gt lt BIND object gt lt BIND Interaction_a gt lt BIND Interaction_b gt lt BIND object gt lt BIND object_short label gt Ade2 lt BIND object_short label gt lt BIND object gt lt BIND Interaction_b gt lt BIND Interaction gt 82 Importing Data Chapter 4 BIND Import Logic Each BIND interaction is defined by the tag lt BIND Interaction gt Each interaction is made up of two components stored between the tags lt BIND Interaction_a gt and lt BIND Interaction_ b gt A reaction object is created in the Vector PathBlazer database for each interaction listed in the file Component objects are created from each component stored in an interaction The following table describes each XML attribute or element for which a value is directly parsed and the anno tation to which it is mapped to an object in the program Annotation in Description Vector PathBlazer lt Interaction id gt Interaction name Reaction Name lt Interaction id gt ID is appended with the text Interact For example Inter act 301 Reaction Crosslink ID is appended with the text BIND INTERACT For example BIND INTERACT 301 Note Components and reactions including components named UNDEFINED UNKNOWN Homo sapiens or an empty value are skipped lt BIND object_short label gt Short label of the object Component Name lt BIND ob
171. gy Categories Enter the query ontology term you want searched in the Find GO Term text box and click the Find button Figure 7 3 Search results as well as the number of terms found display in the left panel If you Click on a line in the results list the term is highlighted simultaneously in the GO tree in the right panel Gene Ontology Hierarchy Browser Find GO Term E mO molecular_function GO 0003674 apoptosis Ge anticoagulant activity G0 0008435 B antifreeze activity 40 00161 2 ant apoptosis GU UU06S16 d UT antioxidant activity G0 001 6209 ant apoptosis G0 000637 6 l 1 apoptosis regulator activity 00 00 apoptosis GU 000631 5 AD apoptosis activator activity 40 apoptosis U OU0691 5 EE bo 1 apoptotic protease activate apoptosis activator activity GU d T apoptosis inhibitor activity GO apoptosis inhibitor activity IGUL l 1 binding G0 0005488 apoptosis regulator activity GO MUD catalytic activity G0 0003824 commitment to apoptosis IDU MD cell adhesion molecule activity G0 DNA damage response signal t MCD chaperone activity G0 0003754 d E chaperone regulator activity IBU IL toskeletal regulator activity IGUL j a SK I Ed gt B i e a e j 7 NK Close Help Figure 7 3 Gene Ontology Browser displaying GO term search results The icons in the displayed tree borrowed from standard GO viewers indicate the relationship in the GO tree A child term can be a subcla
172. he Glycolysis reaction subset Set Max number of steps to 10 141 Vector PathBlazer 2 0 User s Manual Assembled 142 Pathway Set Extra steps to 0 select Ignore Paths through these Components and select the Small Molecules subset Select Don t Pool Components in Subset and select the Small Molecules subset Set Direction to Forward ae ee d db 0 Set Interaction Generality to Unlimited The parameters should look similar to those in Figure 6 4 Build a Pathway E Path Component Subsets Build Pathway ka from Component from Pathway I Ignore Paths through these Components glucose Browse la Small Molecules D Build Pathway ka to Component to Pathway ka Don t Pool Components in Subset pyruvate Browse jg Small Molecules ei Build Pathway through Component Hide these Components fructose 6 phosphate Include Reactions from Subsets WOI Reactions Cul All Reactions e glycolysis Show only connecting components Calculate critical points Connection Length r Pathway Direction Max Number of Steps Extra Steps Direction Interaction Generality 10 0 fa Forward v ju nlimited X Cancel Help Figure 6 4 Building a pathway from one component to another component 11 Click OK to start assembling the pathway A dialog box displays informing you of the short est pathway and the total number of reactions that will display Click Yes to continue
173. he Modeling of Systems Englewood Cliffs N J Prentice Hall 1981 von Bertalanffy L General System Theory Brazilier New York 1968 KEGG Kyoto Encyclopedia of Genes and Genomes is an effort to computerize current knowl edge of molecular and cellular biology in terms of the information pathways that consist of inter acting molecules or genes and to provide links from the gene catalogs produced by genome sequencing projects http fire2 scl genome ad jp kegg 199 Vector PathBlazer 2 0 User s Manual References Goto S Okuno Y Hattori M Nishioka T and Kanehisa M 2002 LIGAND Database of Chemical Compounds and Reactions in Biological Pathways Nucleic Acids Research 30 1 402 4 Kanehisa M and Goto S 2000 KEGG Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Research 28 29 34 Licensing Information BIND Description URL References Academic users may freely download the KEGG data as provided at the GenomeNet ftp site at ftp ftp genome ad jp pub kegg Non academic users may also download the KEGG data from this ftp site as long as they are used for internal research purposes For more information see http fire2 scl genome ad jp kegg kegg5 html The Biomolecular Interaction Network Database BIND is a database designed to store full descriptions of interactions molecular complexes and pathways http www bind ca index phtml Bader GD Donaldson Wolting C Ouellette BF Pawson T
174. he current information to an existing PathBlazer template select the existing template name from the Template Name drop down list Click Next The mapping is executed and a message displays stating the number of components that were mapped If there are conflicts such as two or more genes being mapped to the same compo nent you are prompted to resolve the contradiction i e select only one gene component rela tionship Importing Expression Data with a Template Reminder 168 To import new expression data use the following steps 1 2 Select Tools gt Manage Expression Data gt Import Expression Data In the Define Source screen select an expression data file by clicking the Browse button Me and locating the appropriate file Figure 8 3 In the Use Template field select the template you want to use with the file from the drop down list Click Next Define Source e E x Expression Data File GEES u EK a ATE EEEE EAA EA Use Template Yeast Mapping E Cancel Help Figure 8 3 Selecting an expression template The template contains the component to gene name ID mappings and the data file contains the expression values You can apply one template to more than one data file as long as the data file contains genes that are included in the template The Map screen displays the current mapping contained by the template file Figure 8 4 If necessary edit the component to gene name id mapping If y
175. he first dialog box then select either the Single or Multiple Condition radio but ton in the second dialog box In the Add Conditions dialog box that opens from the Condition Type drop down list scroll to the lt object type gt GO Annotation option From this point on the search differs from that described in the Searching Objects in the Database and Creating Sub sets section Continue as follows Add Condition E x Condition Type Pathway GO Annotation Find GO Term Select GO Term EZE molecular function BD DUUOE ZAI d Zu LA antioxidant actrity GO 0016209 gt fT apoptosis regulator activity 60 0016 d I anticoagulant activity GO 0008435 E I antifreeze activity G0 00161 72 l See SE apoptosi bitor activity IDU L binding G0 0005458 I catalytic activity GO 0003824 1 cell adhesion molecule activity 00 0 I chaperone activity GO 0003754 I chaperone regulator activity G0 003 eT cytoskeletal regulator activity G0 00 Ga ea EGE AE EN KA ed A Evidence Type Any Traceable Author Statement best hi Cancel Help Figure 3 60 The GO Annotation dialog box for adding a GO annotation as a database search condition In the Add GO Condition dialog box that opens from the GO tree in the right panel select the GO term you want to set as a search condition Figure 3 60 If you are not sure where in the tree your term is located enter it in the Find GO Term field in the left panel a
176. he fol lowing are the other restrictions that apply when assembling a pathway in Metabolic View 1 Catalyzing agents are not pooled If the same enzyme occurs more than once in a pathway a label displays for each occurrence 2 Any effecting agents are not drawn to the catalyzing agents Protein protein interactions PPI are not displayed and pathways are not assembled through PPI interactions If a PPI reaction is included in a subset of reactions that are used to assemble a pathway a warning displays and you can select to either proceed without the reaction s or stop the assembly Adding Stepwise Reactions to Pathways 138 Once a pathway is generated you can select a component and ask to see the next level of com ponents connected directly to that specific component that is the next reaction When you select a component one of the options is 1 more step The second level from that option allows you to specify whether the next reaction should come from the reaction subset used to Automatically Assembling Pathways Chapter 6 assemble the original pathway if one was used or from the database of all reactions You can also specify whether you want directed reactions that is the next level is from reactions that have a direction associated with them in the reaction such as metabolic or signal transduction reactions or non directed reactions that is protein protein interactions The interaction gener ality score for pr
177. he same or deeper level of classification For example Component A classified as protein will be merged with component A classified as protein regulatory but not with component A classified as lipid In this case component A lipid will be imported into the PathBlazer database and renamed into A dupl 1 A Merge Options dialog box opens during every import process allowing you to define options for merging the data Figure 4 2 PathBlazer Import E b E Select Merging Options Components merging ld Merge components with known classification with components with unknown classification d Back Cancel Help Figure 4 2 PathBlazer Import Merge Option dialog box You can select the option Merge components with known classification with components with unknown classification If this option is checked Component A classified as protein will be merged with component A classified as unknown You can also select a course of action when entries are encountered that are already present in the selected database Keep properties any duplicate entries in the existing database are ignored Replace properties any duplicate entries in the existing database are overwritten If more than one old component matches one new component they are not merged automati cally Other merge rules for importing components with identical names and different functions then apply Merge Component Rules Componen
178. hoice in disclosing the upstream regulators and downstream targets of each molecule in the regulatory network Connected and integrated with the TRANSFAC Professional database TRANSPATH Professional bridges the gap between extra cellular signal molecules Such as hormones cytokines etc and the genes responding to these triggers The above text is taken from the TransPath website listed below http transpath gbf de schacherer F Choi C Gotze U Krull M Pistor S Wingender E The TRANSPATH signal transduction database a knowledge base on signal transduction networks Bioinformatics 2001 Nov 17 11 1053 7 Licensing Information DIP Description URL References http transpath gbf de The Database of Interacting Proteins DIP is a database that documents experimentally deter mined protein protein interactions This database is intended to provide the scientific community with a comprehensive and integrated tool for browsing and efficiently extracting information about protein interactions and interaction networks in biological processes http dip doe mbi ucla edu Xenarios I Rice DW Salwinski L Baron MK Marcotte EM and Eisenberg D 2000 DIP The Database of Interacting Proteins Nucleic Acids Research 28 289 91 Xenarios Fernandez E Salwinski L Duan XJ Thompson MJ Marcotte EM and Eisenberg D 2001 DIP The Database of Interacting Proteins 2001 update Nucleic Acids Research 29 239
179. hway from a Starting Component on page 139 The ending component is pyruvate the number of pathway steps is nine Nine reactions that are the same as for previous example 1 Select Tools gt Build a Pathway gt Build Discovery Pathway 2 In the Build a Pathway dialog box select the Build Pathway from Pathway checkbox Click the Browse button and locate the pathway Pathway glycolysis 2 Steps or by the name you assigned the pathway when you created it 3 Select the Build Pathway to Component checkbox and enter Pyruvate as the ending component In the Include Reactions from Subset field select the Glycolysis reaction subset Set Max number of steps to 10 Set Extra steps to 0 Select Ignore Paths through these Components and select the Small Molecules subset Select Don t Pool Components in Subset and select the Small Molecules subset Set Direction to Forward a Gr GE a eS eS 0 Set Interaction Generality to Unlimited The parameters should look similar to those in Figure 6 7 x Path r Component Subsets Build Pathway from Component V from Pathway ke Ignore Paths through these Components Pathway glycolysis 2 steps Browse lal Small Molecules D Build Pathway ke to Component J to Pathway le Don t Pool Components in Subset pyruvate Browse bi Small Molecules b Build Pathway through Component Hide these Components Browse Include Reactions from Subsets b WOI Reactions SI All Reac
180. ics Window You will still need to step through the Wizard to do so Saving a pw File to the Database When you open a pw file and want to save its contents to the database the following situations can occur e None of the objects in the file are already present in the database e Some of the objects in the file are already present in the database e AI of the objects in the file are already present in the database Vector PathBlazer determines whether some or all objects in the file are already present in the database and allows you to either use the existing objects in the database or create new objects from the objects in the file Use the following steps to save the contents of a pw file to the data base 1 Open the pw file by selecting File gt Open clicking the Open button UZ on the toolbar or selecting a recently opened pw file from the list at the bottom of the File menu The Graph ics window displays the contents of the file Select File gt Save or click the Save button on the toolbar The Save dialog box opens to the screen for naming the pathway Note that the radiobuttons in the Save to box and the Name field are not available Select the Save as new pathway checkbox to make these options available To save the contents of the pw file to the database select the Database radio button and select a pathway subset from the drop down list Name and annotate the pathway and reac tions as described in step 4
181. id gt lt BIND Interaction_a gt lt BIND object gt lt BIND object_short label gt Ade2 lt BIND object_short label gt lt BIND object_other names gt lt BIND object_other names_E gt 03293 lt BIND object_other names_E gt lt BIND object_other names_E gt YOR3293 lt BIND object_other names_E gt lt BIND object_other names_E gt YOR128C lt BIND object_other names_E gt lt BIND object_other names gt lt BIND object_origin gt 1 http www binddb org 81 Vector PathBlazer 2 0 User s Manual lt BIND object origin gt lt BIND object origin_org gt lt BioSource gt lt BioSource_org gt lt Org ref gt lt Org ref_taxname gt Saccharomyces cerevisiae lt Org ref_taxname gt lt Org ref gt lt BioSource_org gt lt BioSource gt lt BIND object origin_org gt lt BIND object origin gt lt BIND object_origin gt OR lt BIND object_origin gt lt BIND object origin gt lt BIND object origin_ chem gt lt BIND chemsource gt lt BIND chemsource_names gt lt BIND chemsource_names_E gt LY294002 lt BIND chemsource_names_E gt lt BIND chemsource_names_E gt 2 4 Morpholinyl 8 phenyl 4H 1 benzopyran 4 one lt BIND chemsource_names_E gt lt BIND chemsource_names_E gt 2 4 morpholinyl 8 phenochrome lt BIND chemsource_names_E gt lt BIND chemsource_names gt lt BIND chemsource_chemical formula gt C19H17NO3 lt BIND chemsource_chemical formula gt lt BIND chemsource gt lt BIND object ori
182. ify a component to build from to or through as well as other parameters Vector PathBlazer then evaluates all the specified reactions and automatically constructs a pathway or network in the Graphics window that includes all possible pathways and interactions that match the query 133 Vector PathBlazer 2 0 User s Manual Pathway Assembly Parameters There are two steps in the assembly process First you create component and reaction subsets to limit the pathway assembly output This is key to building a meaningful pathway Second you specify the parameters that must be considered when building the pathway Specifying Parameters The Build a Pathway dialog box is used to configure a query by which Vector PathBlazer will automatically build a pathway Figure 6 1 To open this dialog box select Tools gt Build a Path way and select either Build Metabolic Pathway or Build Discovery Pathway from the sub menu The dialog box is the same for Metabolic and Discovery pathways but the results presented in the Graphics window are different e When a pathway is built in Discovery View any enzymes included in the results display as separate components and are pooled Pooling means that if the enzyme or other component is included in more than one reaction in the pathway it is represented only once in the Graphics window Connectors are drawn from the single component to any reactions that reference it e When a pathway is built in Metabolic
183. igure your connection settings and to enter server proxy information if a firewall is used at your site See the Internet Connection Set tings section on page 188 for more information For information on the Test Connection button see page 188 Once you have configured the Dynamic License dialog box parameters to set all Vector appli cations to Dynamic License press the Set For All Applications button Once you do this when you Close this dialog box the Applications tab now shows Dynamic License for all applications Note When you set Dynamic licenses for all applications this operation only applies for those applica tions for which you do not have a Static License Press the Apply button to execute the dynamic license configuration Trial License Dialog Box To configure a trial license click the Trial button at the bottom of the Applications tab of License Manager Figure A 3 This opens the Trial License dialog box Figure A 6 Trial License Mame osh Brown Organization Gete Phone number 240 846 3398 E mail address JLbrown dotcomcom For a free tral of applications please e mail your Hardware IDF Company Name and Address to tial informasinc com HIGA trial informasine com sntitrialentitrial cgi Default UAL Internet Connection Settinas Set for all applications Test Connection ea Figure A 6 Trial License dialog box in License Manager Enter your name the name of your organization pho
184. inase gt glucose 6 phosphate ADP Reaction 2 glucose 6 phosphate glucose phosphate isomerase gt fructose 6 phosphate Reaction 3 fructose 6 phosphate ATP phosphofructokinase gt fructose 1 6 bisphosphate ADP 1 2 on Se 2 Pl 10 11 12 Select Tools gt Build a Pathway gt Build Discovery Pathway In the Build a Pathway dialog box select the Build Pathway from Component checkbox and enter Glucose as the starting component Select the Build Pathway to Component checkbox and enter Fructose 6 phosphate In the Include Reactions from Subset field select the Glycolysis reaction subset Set Max number of steps to 3 select Ignore Paths through these Components and select the Small Molecules subset containing the small molecules ATP ADP and H20 Select Don t Pool Components in Subset and select the Small Molecules subset Set Direction to Forward Set Interaction Generality to Unlimited The Build a Pathway dialog box should look like that in Figure 6 2 Click OK to start assembling the pathway The assembled pathway that displays in the Graphics window consists of the first three steps of glycolysis Figure 6 11 E Automatically generated pathway 6 Discovery unrestricted view Database b ATP Figure 6 11 First three steps of glycolysis automatically assembled Once the pathway is assembled the next reaction can be added by searching either the database for all reactions or
185. ing connectors in reactions in a forward direction or in the direction connectors point For example in the biological sense as well as in the way it is represented in Vector PathBlazer glycolysis proceeds from glucose to pyruvate ina series of steps and the connectors in the reaction are represented in a left to right pointing direc tion glucose gt glucose 6 phosphate etc If this pathway were built in a forward direction the program would follow the connectors in each reaction from glucose to pyruvate Backward the pathway backbone is constructed by following connectors in a backward direc tion or against the direction connectors point For example in the biological sense glycolysis does not run in a backward direction from pyruvate to glucose However if the program is instructed to build a pathway in the reverse direction from pyruvate to glucose it will build against the direction connectors point Ignore direction the pathway backbone is constructed without considering direction Consider the following examples in terms of the pathway pak o parr lf the program is instructed to assemble a pathway from Gen step e B in two steps in the forward direction then only the one step pathway is returned because the program goes in the direction of the connectors from B to C but in the next reactions between C and D and E the connectors point in the opposite or back wards direction so the program does not consider these reactions
186. ing is Unlimited If Unlimited is selected all possible interactions regardless of biological relevance are shown Pathway Colors in the Graphics Window When you are building a pathway in the Graphics Pane pathway elements display in the follow ing default colors Through Component in the Build pathway aqua through component field Start component Component from which pathway aqua begins End component Component with which pathway red ends Shortest new path Shortest new path or first path deep aqua from which a pathway begins All other new paths Secondary or paths other than teal to dark blue shortest new path Critical points Critical points in the pathway Components not Components that are not directly nocolor involved in any path involved in a pathway or reaction but are involved in a peripheral way such as a catalyst Assembling Metabolic Versus Discovery Pathways When you draw a pathway in Metabolic View in the Graphics window and you want to include a catalyzing enzyme with a connector represented as a double headed arrow the catalyzing reaction is included as a label of the reaction Similarly when Vector PathBlazer automatically assembles a reaction in Metabolic View any catalyzing connector that links to a reaction node is drawn as a label of the reaction In Discovery View on the other hand the connector and the catalyzing agent that is the enzyme are drawn as separate elements in the reaction T
187. ing with Invitrogen Life Science Software is that the bio informatics software packages are designed to integrate with each other Vector PathBlazer 2 0 includes tools for directly accessing expression data in Vector Xpression 3 1 and Vector Xpres sion 3 1 contains tools for exporting gene expression data directly to Vector PathBlazer 2 0 Vector PathBlazer 2 0 is integrated with Vector Xpression 3 1 with the following features From Vector PathBlazer 2 0 e You can automatically create a template that maps expression data to pathway compo nents The template is used to import expression data into PathBlazer See Creating an Template Automatically on page 166 e You can launch a search in Vector Xpression 3 1 for chips expression runs and experi ments containing genes coding for components of a specific pathway See Searching a Vector Xpression Database on page 176 e For a specific expression experiment in PathBlazer you can open a corresponding object in Vector Xpression if the experiment originated in Vector Xpression See Opening an Experiment in Vector Xpression on page 177 From Vector Xpression 3 1 e You can automatically create a template that maps expression data to pathway compo nents The template is used to import expression data into PathBlazer See Creating a Template from Vector Xpression 3 1 on page 1 6 e You can send expression data directly to PathBlazer using the template you have cre ated See Sending Expression
188. ions e by adding existing reactions in the database e by adding existing pathways in the database Pathways can be drawn in two different kinds of modes or views Metabolic and Discovery The main difference between these two views is how catalyzing agents that is enzymes and protein protein interactions are displayed e In Metabolic View the enzyme is not graphed as a separate element and the reaction that includes the enzyme is not graphed as a separate connector Instead the enzyme is drawn as a label of the reaction node The enzyme is still an independent object in the database and is selected from the database but is displayed close to the reaction node e In Discovery View the enzyme is drawn as a separate component of the reaction and is connected to the reaction node by a double headed arrow to indicate that the enzyme is catalyzing the reaction 109 Vector PathBlazer 2 0 User s Manual Hexokinase D Glucase i Du Glucose 6 phosphate KO ba b D Glucose _ amp D Glucose b phosphate Metabolic View Discovery View Note Protein protein interactions can only be drawn in Discovery View Drawing Tools 110 The Palette window contains a set of drawing tools that include shapes for representing compo nents and lines for representing connectors Figure 5 7 Shapes lt gt lt a for drawing Physical Lipid DNA RNA Enzyme components E b E Protein Undefined H20 Mormal a
189. is included in the default database that is installed with Vector PathBlazer and is located in C VNTI Database PathwayDB DeRisi_glycolysis_exp_import txt DeRisi JL Iyer VR and Brown PO 1997 Exploring the metabolic and genetic control of gene expression on a genomic scale Science 278 5338 680 86 Interaction Generality 202 Saito R Suzuki H and Hayashizaki Y 2002 Interaction generality a measurement to assess the reliability of a protein protein interaction Nucleic Acids Research 30 5 1163 68 General Problem Solution Problem Solution APPENDIX TROUBLESHOOTING This appendix contains a list of troubleshooting tips to aid in solving problems you might encounter when using Vector PathBlazer When a new component is created from one of the shapes in the Palette window and is named a name other than the one entered displays in the Graphics window When a component is added the program searches the existing components in the database by name and by synonym for a match If the entered name is a synonym to an existing component then the primary name of that component displays Right click on the object and select Change Component Display Name In the dialog box that opens select the display name from those listed You can select an option to change the name in the current image or to change it in all pathways When trying to add a new component that does not already exist in the database by primary name or
190. ism meth ods etc for components and reactions Some additional information is entered into external crosslinks reference xml References to scientific publications are extracted from this file They are stored inthe descrip tion field location xml This file contains information about subcellular location This information is stored in component and reaction location fields hyperlinks xml This file contains links to external databases for molecules and reactions Custom Dictionaries There are two TransPath custom dictionaries created in Vector PathBlazer classDict and organDict These dictionaries are supplied with PathBlazer and they are text tab delimited files The file classDict contains the dictionary that translates classes of molecules as they are defined in TransPath into an internal PathBlazer classification File organDict translates names of organisms according to TransPath usage into PathBlazer names There is no need for the ordinary user to modify or amend these files but an advanced user may want to change the classification mapping 95 Vector PathBlazer 2 0 User s Manual Instructions for Importing TransPath Data You can import data either into the default PathBlazer database or into a new separate database you create before the data import To create a database see Creating a New Database on page 10 You must also have downloaded the data file described in JransPath Source Files on page 93 to your loca
191. isplay You can display the name of a reaction or show information about a connector with a label Labels can 131 Vector PathBlazer 2 0 User s Manual be added to a component reaction node or connector to display additional information or titles about one of these objects A label is not a separate object but is linked to the object to which it is associated in a particular pathway and is saved with the pathway Create a label by selecting an object in the Graphics window and selecting Create Label from the shortcut menu An untitled label is placed near the selected object Name the label and press ENTER The label displays next to object Figure 5 28 Labels can be moved anywhere in the Graphics window by selecting the label and dragging it to a new position When selected a dotted line shows the object to which the label is connected Delete a label by selecting it and pressing the DELETE key Change a label s display properties by selecting it and selecting Object Properties from the shortcut menu or using the graphics buttons in the Graphics toolbar Protein Undefined v H20 Normal Interaction Catalysis E Activation E ZG New PathWay 1 Discovery unrestricted view Database iol Labels Glucose ATP reaction 1 rro reaction 2 Glucose 6 phosphate a dE 6 phosphate ADP a EA Fa Glucose 6 phosphate isomerase Master View Figure 5 28 Lab
192. isplayed at the same time in the List Pane and then selecting Create Component Subset from the shortcut menu In the Create Component Subset dialog box that opens enter a name and description for the component sub set and click Create All components included in the selected reactions or pathways are added to the new subset Reversing the Direction of a Reaction In Vector PathBlazer two reactions are required to represent a reversible reaction one reaction in which a group of components are substrates and another group are products and a second reaction in which the substrates and products are switched In some cases you may want to reverse the direction of a reaction that is make the substrates products and vice versa without rebuilding the reaction from scratch If you want to swap the substrates for products in an imported reaction you can easily reverse the reaction in Vector PathBlazer When the direction of a reaction is reversed a new reaction is created in the database Use the following steps to reverse the direction of a reaction 35 Vector PathBlazer 2 0 User s Manual Note 1 Select the reaction in the List Pane of the Database Explorer To display it in the Graphics window double click on it or select Open from the shortcut menu In the following example the reaction in Figure 3 33 is reversed Methy ladenine Methyladenosine D Ribase H20 Figure 3 33 Reaction as it displays in Graphics window before it is
193. iur luzee io Ea igi test ZG INTERACT 4162 BIND Sec13 Ycr099c Ea ial GEO jbh ZG INTERACT 4163 BIND Sec13 Ydl166c ee a l 3 INTERACT 4164 BIND Sec13 Sec31 E o eee 3 INTERACT 4165 BIND Sec13 Nup145 ZZ edi TT I INTERACT 4166 BIND Ylr218c Pdb1 7 A All Gra KA INTERACT 4167 BIND Ylr22 ic pri115w E B EA E Sie A 4 gt Current Database C Documents and Settings jill INFORMAXINC My Documents My PathBlazer Data PathBlazer PathBlazer_demo_db mdb i NUM Figure 3 47 Crosslinks display in the shortcut menu of an object in the Graphics window The G protein Stimulatory Gs pathway that is pre loaded into the default Vector PathBlazer database is configured with links to corresponding molecules in the VNTI Advance database The components in the Gs pathway that are linked are e Adenylate cyclase to ADCY e Beta adrenergic receptor to ADRA1A e Raf to RAF e Phosphodiesterase to PDE1A e GRK to GPRK2L e MAPK to MAP2K1 e B Raf to BRAF Working with Pathways Chapter 3 e Epac to EPAC Searching the Database There are two ways to search the database for specific objects e Search the pathway displayed in the Graphics window for components and reactions by name e Search the entire database for components reactions and pathways by name and or by annotation When you search the entire database you can also create subsets from the search results Finding an Object in a Pathway You might create a pathway that be
194. ively Known to be in certain organisms locations but it cannot or has not been definitively determined whether it is known to be in other organisms locations For example you might definitively determine from a Western blot that ERBA the ERBA receptor is present in the nucleus but you cannot experimentally determine whether it is present in the ER In Vector PathBlazer the subcellular value for the component ERBA would be lt Location Known In Nucleus gt Not In is the opposite of Known In and means that an object is definitively known to not be in certain organisms locations but it cannot or has not been definitively determined whether it is not known to be in other organisms locations Based on the above definitions of In Known In and Not In Strict Search means that only objects that are assigned the value of In or Known In are returned When an organism location is assigned the value of In a 7 is attributed to that organ ism location and a 0 is attributed to all other organism locations for the purpose of the search When an organism location is assigned the value of Known In a 1 is attributed to that organism location and no value is attributed to all other organism locations When an organism location is assigned the value of Not In an 0 is attributed to that organism location and no value is attributed to all other organism locations Non Strict Search also means that objects that are assigned the value of In or Know
195. izing column display in Database Explorer Rearrange columns by selecting a column name in the Column Settings box and clicking Move Down or Move Up In the List Pane you can also drag the Description or Formula col umn headers left or right The Name column is fixed and cannot be reordered 32 Working with Pathways Chapter 3 Naming Copying and Deleting Objects In Vector PathBlazer the unique identifier of an object is its name or its primary name and there can be only one object in the database with a particular primary name Components can have synonyms or alternative names as secondary names While a primary name can only be associated with one object a synonym can be associated with more than one object For example you might want to enter the stereoisomers of a sugar such as D and L glucose as separate components in the database Then you might assign the synonyms glucose and mannose to them As you will learn more about in Chapter 5 Drawing Pathways you can add a component that already exists in the database to the Graphics window and Vector PathBlazer will search the database by primary name and by synonym to retrieve the component from the database All components that match by name or synonym will be listed in the search However the primary name and not the synonym displays in the Graphics window when components are drawn and when they are listed in the Database Explorer When renaming copying or
196. ject_short label gt Example ATP S4 HSP70 lt BIND object_other names_E gt Synonyms Component Synonyms lt BIND object_other names_E gt lt Org ref_taxname gt Species Component Organism lt Org ref_taxname gt lt BIND chemsource_chemical for Chemical formula Component Chemical Formula mula gt lt BIND chemsource_names_E gt Component Synonyms lt BIND object type id_protein gt or Component type Component Type or Subtype lt BIND object type id_dna gt or lt BIND object type id_rna gt or lt BIND object type id_small mole cule gt or lt BIND object type id_complex gt or lt BIND object type id_gene gt or lt BIND object type id_photon gt Link to GI database Component CrossLink lt BIND other db_dbname gt and Link to other databases for Component CrossLink lt BIND other db_strp gt small molecules lt BIND cellstage_phase gt Cell cycle phase Component Locations lt BIND gen place gt General cellular location Component Locations where an interaction takes place Table 4 4 XML attributes and elements in the BIND _interaction xml file that are imported 83 Vector PathBlazer 2 0 User s Manual Ge Annotation in lt BIND membrane gt Description of a location in Component Locations a lipid bilayer membrane lt BIND path descr_descr gt Description of the compo Component Comments nents lt BIND descr_simple descr gt Description of the reaction Reaction Comments Table 4 4 XML attribu
197. ked the layout converts to a zoomed out mode To zoom in to the graphics use any of the zoom features described on page 17 Layout Properties The parameters in the Layout Properties dialog box determine the settings for each type of lay out Open the Layout Properties dialog box by selecting Layout gt Properties Each type of lay out corresponds to a tab in this box that contains the layout s settings Circular Tab The Circular layout settings display in Figure 3 22 and are described in Table 3 7 Layout Properties E E E ZO Circular ep Hierarchical Be Symmetric Limit Cluster Size la Min A W Max 20 Spacing Cluster Alignment Proportional Spacing f Center Top Bottom C Constant Spacing Between Nodes 500 Between Clusters Tangential EI Radiat IE Cancel Layout Reset Defaults Help Figure 3 22 Circular Tab of the Layout Properties dialog box Limit Cluster Size Minimum and maximum number of nodes allowed in a cluster Defaults are Min 4 and Max 20 Spacing Proportional Spacing Creates space around nodes propor tional to node size Recommended as the default setting Constant Spacing Creates space around nodes that is the same for all nodes Between Nodes Value between nodes Between Clusters Dictates spacing between clusters on Values Tangential the circle around the main cluster Radial and between the clusters Cluster Alig
198. king the Add button In the Add Condition dialog box select a GO term in the right panel Figure 7 6 or launch a search for a gene ontology term of interest by entering the term in the Find GO Term text box Select the term in the results panel this simultaneously selects it in the right panel GO Annotation Select Term and Provide Attributes Find GO Term Select GO Term Tr ZE biological_process GO0 0008150 E I behavior G0 0007610 T biological_ process unknown ZOO SE Ij cellular process GO 0009987 EES cell communication G0 00071 AL cell adhesion GO 000715 cell cell signaling 00 0007 host pathogen interaction Induction of an organ IDU pollen pishl interaction GO response to extracellular sti aignal transduction 40 00 2 JU I al e TN ee eee TN edi source DD Unique ID in DE Evidence Type Organism Traceable Author Statement b el ei Add Cancel Help Gei Figure 7 6 In the GO Browser click on a GO Annotation to assign to an object and click Add Click the Add button and the selected annotation is loaded into the GO Annotations tab of the Properties dialog box The other two buttons on the GO Annotations tab Edit Delete do not become available until you select the bottom leaf in the tree 158 Gene Ontologies Chapter 7 Edit a gene ontology annotation by selecting the bottom leaf on the annotation tree on the GO Annotations tab and clicking the Edit button In the
199. ks synonyms type group _name list_of_subcomponents definition _of_locations list_of_ pathways _names list_of_annotations list_of_reference_accesses 191 Vector PathBlazer 2 0 User s Manual comments list_of_ formulas gt lt ATTLIST substance ID ID FREQUIRED gt lt Description of OriginAccess gt lt ELEMENT list_of_origin accesses origin access gt lt ELEMENT origin _access type_of data database access item_ URL extra_data gt lt ELEMENT type_of_data HPCDATA gt lt ELEMENT database 4PCDATA gt lt ELEMENT access PCDATA gt lt ELEMENT URL PCDATA gt lt ELEMENT extra_data HPCDATA gt lt ELEMENT synonyms name gt lt NUTOKENS s string is represented like class subclass gt lt ELEMENT type NMUTOKENS gt lt distributed ontology table gt lt ELEMENT group_name PCDATA gt lt ELEMENT list_of_subcomponents name gt lt ELEMENT list_of_locations location gt lt Description of Location gt lt ELEMENT location species tissue celltype cell_ compartment stage gt lt ELEMENT species NMTOKEN gt lt IATTLIST species Op CDATA REQUIRED gt lt ELEMENT tissue NMTOKEN gt lt IATTLIST tissue Op CDATA REQUIRED gt lt ELEMENT celltype NMTOKEN gt lt IATTLIST celltype Op CDATA REQUIRED gt lt Description of CellCompartment
200. l file system Use the following steps to import TransPath data into the Vector PathBlazer database 1 Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 2 From an open PathBlazer window select File gt Import The PathBlazer Import tool opens displaying the various import options Figure 4 13 PathBlazer Import a b x Select import module Import User PPI data Import DIP data Import KEGG v 26 data Import TransPath data SERA branch of data from hal File Description E data from TransPath database Hent gt Cancel Help Figure 4 13 TransPath file selected for import 3 Choose Import TransPath Data The Description box reflects the type of data chosen for import Click Next 4 In Screen 2 of the Import Wizard in the Root Folder field locate the root folder storing the multiple TransPath files by clicking the Browse button Figure 4 73 Select the correct folder in the Browse for Folder dialog box and click OK The complete path to the root folder file displays in the Root Folder field PathBlazer Import E E E W Create reverse reactions for bidirectional reactions a Root folder FO Browse b Molecule file molecules OO Browse SO Gere file eresi Browse Reaction file reactions O Browse e b Annotate file annotates O Browse 4 Location file locations O Browse Hyperlink fil
201. lder by selecting a folder in the Contents or List Pane select the Components Reactions Pathways folder if there are no other folders and then selecting Create Folder from the shortcut menu Name the folder and press ENTER Delete a folder by selecting it in the Contents or List Pane and then selecting the Delete but ton x on the Explorer toolbar or Delete from the shortcut menu Click Yes in the confirma tion dialog box Creating Subsets Note Subsets can only contain one object type For example a subset created in the Components folder can only contain components When a subset is selected in the Explorer Contents Pane the number of objects in the subset and displayed in the List Pane displays on the status bar Subsets are contained in folders and cannot be contained in another subset When creating a subset from the List Pane you can either create an empty subset or you can select objects and add them to a new subset You can also create a subset based on search results For more information about searching the database see Searching Objects in the Database and Creating Subsets on page 54 If you try to assign a name already given to an existing subset you will be informed that you must specify a different name Create an empty subset by selecting a folder in the Contents or List Pane and then selecting Create Subset from the shortcut menu A subset initially called New Subset is added to the List Pane Name the subs
202. lect Don t Pool Components in Subset and select the Small Molecules subset Se Yt ee en Set Direction to Forward 150 Automatically Assembling Pathways Chapter 6 10 Set Interaction Generality to Unlimited The Build a Pathway dialog should look similar to that in Figure 6 9 11 Click OK to start assembling the pathway 12 Once the pathway is assembled right click on Hex A hexokinase in the Graphics window and select Add reaction from the shortcut menu 13 In the Add reaction dialog box select Output PPI and the reaction subset All Reactions to search the entire database Click Search 14 The Add Reaction dialog box displays all reactions in which Hex A is included Figure 6 17 Select one or more reactions by selecting the checkbox next to a reaction and click OK Add Reaction E x Matching Reactions INTERACT 27479 1 GM130 Hert INTERACT 39136 1 Hex A CG9993 INTERACT 39134 4 Heuk CGES76 INTERACT 39135 S He BG 0500160 10 Show Reachons with Generality Lal zaire Ea Figure 6 17 Add Reaction dialog box lists all reaction in which selected component is included Assembled The selected reaction is added to hexokinase Figure 6 18 Any components in the added reac Pathway tion that are already displayed in the pathway are pooled when the reaction is added Hex A added reaction Figure 6 18 Adding reactions to Hex A hexokinase 151 Vector PathBlazer 2 0 User s Manual 1
203. llowing reaction will be reconstructed beta D glucose ATP gt glucose 6 phosphate ADP catalyzed by Hexokinase GLC corresponds to beta D glucose in the compound dat file ATP to ATP GLC 6 P to glu cose 6 phosphate etc The enzyme Hexokinase is described in the enzymes col file The reaction will be named R81 RXN File enzrxns dat This file contains information about enzymatic reactions The reaction is constructed from data stored in this file as well as from references made to other files of BioCyc Only information which is different from that stored in the reactions dat file is loaded from the enzrxns dat file An entry from this file is shown below UNIQUE ID ENZRXN7E 124 TYPES Enzymatic Reactions COMMON NAME glucokinase BASIS FOR MANUAL ASSIGNMENT ENZYME GLK MONOMER REACTION GLUCOKIN RXN BioCyc Pathways File BioCyc databases store information about pathways Pathways are stored as pathway objects in the PathBlazer database 90 Importing Data Chapter 4 File pathways dat One pathway from this file is shown below UNIQUE ID TYPES COMMON NAME PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS PREDECESSORS REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REACTION LIST REA
204. lucose ATP amp beta D glucose 6 phos phosphate ADP phate ADP TREDEGLOW PWY 1 GLK MONOMER File genes col and genes dat These two files contain description of genes Components in PathBlazer are created The name of an entry is augmented with gene These components have class DNA gt Chromosome gt Gene 87 Vector PathBlazer 2 0 User s Manual 88 The following is an example of a genes col file entry ZNTA zntA zinc transporting ATPase ECOLIO157 4392922 4395120 UNCLASSIFIED The corresponding entry in the genes dat file UNIQUE ID ZNTA TYPES Unclassified Genes COMMON NAME zntA CENTISOME 79 46035 POSITION COMMENT Residues 1 to 732 of 732 are 98 90 pct identical to residues 1 to 732 of 732 from Escherichia coli K 12 Strain MG1655 B3469 COMPONENT ECOLIO157 OF LEFT END 4392922 POSITION PRODUCT ZNTA MONOMER RIGHT END 4395120 POSITION TRANSCRIPTION DIRECTION The name of the component is taken from the COMMON NAME field A UNIQUE ID and first column in the genes col file will be added to the synonyms list The content of PRODUCT filed will be added to the description The start and end of the gene described in LEFT END POSI TION and RIGHT END POSITION will be entered into the description File protcplxs dat This file contains information about protein complexes It is in tabular format They are stored as components in PathBlazer database An entry from this file CPLX7E 9 glycine tR
205. ly into two sections 1 how to import and use the Gene Ontology terms file and 2 how to import and use the Gene Ontology Annotations file Before you can import any gene ontology files you must download them to a local directory 153 Vector PathBlazer 2 0 User s Manual e File 1 Gene Ontology dictionary of terms Download to a local directory the most recent xml file from http Awww godatabase org dev database archive latest See Intro duction to Gene Ontologies in the following section e File 2 Gene ontology annotations file containing GO terms that are already mapped to genes in a given organism Select and download to a local directory the specific annota tion file you want to use from _ http Awww geneontology org GO current annota tions shtml Note To import this file you MUST import File 1 GO terms first Then see Importing Gene Ontology Annotations on page 159 Note After you have downloaded gene ontology files from the Consortium website you will need to return to the GO website for periodic updates to your ontologies See Updating GO Categories on page 159 As the gene ontology annotations dictionary is imported annotations can be assigned to Path Blazer objects Alternatively from within PathBlazer you can manually assign specific gene ontology terms to individual PathBlazer components reactions and pathways or in some instances you can annotate objects in batches You can group together in a subset obje
206. m tumefaciens log_op 196791 gt lt organism Class 0 Name Anabaena sp log_op 154138064 gt lt organisms gt lt substance gt Defining Reactions The second part of the file contains a list of interactions that is reactions and the attributes of each reaction For each reaction described between the lt reaction gt attribute a reaction object is created in the database with the unique ID that is included in the lt reaction ID gt element Each of the attributes between the lt reaction gt attribute describe annotation of the reaction Components in a reaction are included in the lt agent ID gt element If a reaction is directional the lt role gt attribute contains educt to indicate the component is a substrate of the reaction or product to indicate the component is a product The actual reference to the component in the component part of the file is included in the lt substance ref gt element Each connector in the reaction is defined in the lt conf_arc gt attribute which describes the from component to its appropriate reaction lt list_of_interactions gt lt reaction ID Gly 1 DB Descr Type unknown gt lt BioNet ID Gly 1 gt lt list_of_agents gt lt agent ID 3 ADP 2 phosphoglycerate gt lt role gt educt lt role gt lt substance ref 3 ADP 2 phosphoglycerate gt lt agent gt lt agent ID Phosphoenolpyruvate gt lt role gt product lt role gt lt substance ref Phospho
207. me by clicking the Browse button and selecting a component from one of the component subsets in the database or you can enter the name of the component in the text field Synonyms can also be entered in the text field Select a reaction subset by selecting from the options in the drop down list under Include Reactions from Subset To use all reactions in the database select the All Reactions subset Only reactions present in the selected subset are considered during the assembly For example if a reaction subset is selected that contains reactions that only occur in the human only those reactions that is valid in human are used in assembling the pathway Using Component Subsets to Limit Pathway Interactions The Component Subset box in the upper right of the Build a Pathway dialog is for specifying which components you want to exclude pool or hide when assembling pathways In addition to specifying the start and end components you can identify component subsets to be excluded from the pathway during assembly This is an effective way to reduce the number of reactions in the display For example if you create a subset of common components such as water ATP UTP etc you can specify that these should be excluded from the pathway assembly and the pathway will be constructed without creating paths through these components Excluded components if they exist in reactions are shown in the pathway but are not used in linking reactions togethe
208. mponent Select component from database Database Component GS Figure 5 4 Wizard for creating new components 114 Drawing Pathways Chapter 5 4 Enter general information to name and describe the component in each of the fields Figure 5 5 Only the Name field is a required field Click Next Component 2 x Mame Datasource FO Chemical Formula P Source P el Disease FO Description lt Back Cancel Help Figure 5 5 Wizard for creating new components adding general information 5 Select the Component Class from the drop down menu Figure 5 6 Available fields differ depending on which type of component is selected from the Component class field Enter information about the component s type in each of the fields The type and subtype if avail able are automatically entered depending on the selected shape Click Next Component Class i x Component class Protein e Protein subclass Enzyme EC Number Genenc Name lt Back Cancel Help Figure 5 6 Wizard for creating new components defining a component s type 6 Enter information about the component s location Figure 5 7 or organism source Click the Add button to add a location or organism source and fill in the Type Tissue and Subcellu lar Location and Name fields Figure 5 7 More than one location can be added by clicking Add to add each additional location Once a row is added click Edit to change the info
209. mponents and parameters the expected output instructions for assembling the path way and how the assembled pathway displays in the Graphics window Before You Begin Create a reaction subset that contains all of the reactions in the glycolysis pathway In the All Pathways folder in the Database Explorer right click on a glycolysis pathway and select Create Reaction Subset Name the subset Glycolysis and click Create Each of the examples in this section uses a filter applied to a small molecule subset that includes H20 ADP and ATP This Small Molecule subset loads with the PathBlazer demo data base Building a Pathway from a Starting Component Description Input Output Steps This example describes how to assemble a pathway by entering a from component only Starting component is Glucose number of pathway steps is three Reaction 1 Glucose ATP hexokinase gt glucose 6 phosphate ADP Reaction 2 glucose 6 phosphate glucose phosphate isomerase gt fructose 6 phosphate Reaction 3 fructose 6 phosphate ATP phosphofructokinase gt fructose 1 6 bisphosphate ADP 1 Select Tools gt Build a Pathway gt Build Discovery Pathway 2 Inthe Build a Pathway dialog box select the Build Pathway from Component checkbox and enter Glucose as the starting component 139 Vector PathBlazer 2 0 User s Manual Assembled 140 Pathway Uncheck the Build Pathway to Component checkbox In the Include Reac
210. mporting Data Chapter 4 4 Inthe BIND Settings dialog box select the BIND_Interaction xml file for import by clicking the Browse button Locate the corresponding file in the Open dialog box and click Open The complete path to the file displays in the Select source file field Figure 4 10 PathBlazer Import E b Ea Select source file D Pathe lazersBINDABIND Interaction xml Browse lt Back Cancel Figure 4 10 BIND file selected for import Click Next In the Merge Option box see Figure 4 2 select the merge options For more information see Merge Option Dialog Box on page 67 7 To import the data click Next The Load BIND dialog box opens and displays the progress of the import To stop the import click Cancel 8 A message displays when import is successfully completed Click Close Since BIND data only contains information about interactions between two components there are no predicted products and each BIND interaction is represented as a one sided equation Importing BioCyc Data BioCyc at the time of this writing is a collection of 17 bioinformatics databases that describe the genome and the characterized biochemical machinery of model organisms whose entire genomes have been sequenced such as Escherichia coli Homo sapiens and Agrobacterium tumifaciens For instance in the case of Escherichia coli the EcoCyc database describes the mechanisms of transcriptional regulation of E coli genes and
211. n In are returned Important In a Non Strict Search objects that are assigned no value for location organism are also returned The following are some example search conditions using Strict and Non Strict settings 56 ERBA is in the nucleus Therefore it is not in the ER In Vector PathBlazer values are set to lt nucleus 1 gt and lt ER 0 gt Both a strict and a non strict search for lt Location Note Working with Pathways Chapter 3 Nucleus gt return ERBA Both a strict and a non strict search for lt Location ER gt do not return ERBA e ERBA is known in the nucleus Therefore it is not Known if it is in the ER In Vector Path Blazer values are set to lt nucleus 1 gt and lt ER no value gt Both a strict and a non strict search for lt Location Nucleus gt return ERBA A strict search for lt Location ER gt does not return ERBA However a non strict search for lt Location ER gt does return ERBA e ERBA is in the nucleus and in the ER In this case it is definitively Known to be in two locations Even though it is known to be in two locations it is still not in any other loca tions In Vector PathBlazer values are set to lt Nucleus 1 gt and lt ER 1 gt Both a strict and a non strict search for either lt Location Nucleus gt or lt Location ER gt return ERBA A similar situation occurs if more than one value is known in a location organism e ERBA is notin the nucleus Again it is n
212. n direction or resulting product In protein protein interactions the reaction node is hidden and the connector between two protein components is represented as a straight line The following example shows a protein protein interaction hol A Mal D Figure 3 6 This protein protein interaction is the customary way to represent PPI reactions This example hav ing no product is equivalent to the first example in Figure 3 5 these two reactions will have the same represen tation in the database The first reaction in glycolysis is shown in Figure 3 7 The entire reaction is outlined with a dot ted line to emphasize that a reaction is made up of components connectors and a reaction node The input components in the reaction are glucose and ATP and the output components are glucose 6 phosphate and ADP The connectors from glucose and ATP to the reaction node point to the node indicating they are substrates The connectors to glucose 6 phosphate and ADP point from the reaction node indicating these components are products of the reaction The double headed arrow between hexokinase and the reaction node indicates that the enzyme catalyzes the reaction Ei vector PathBlazer 2 Glycolysis Pathway File Edit View Tools Layout Window Help EEE D ai Poa aja olala Er Arial ior Z UJA ba Sm ww h i SO Glycolysis Pathway Discovery unrestricted view Database B ZA Physical Glucose Reaction
213. n displays To view the specifics of the List Condition select the item then click the Edit button You can specify only one set of multiple conditions for a search Once you add a multiple condition set the Add Multiple Condition button becomes unavailable The conditions making up a multiple condition set are searched with the OR operator See the following section Custom Search Logic One multiple condition can be combined with several single conditions however 57 Vector PathBlazer 2 0 User s Manual e To edit a condition select it and click Edit For a multiple condition set this will display all of the search term values represented by the Name List Condition phrase e lo delete a condition select it and click Delete e To add additional search conditions click Add lt single multiple gt Conditions buttons again select from the available fields and enter values The condition identifier increases by one with each new condition C2 C3 etc Custom Search Logic Note Note For multiple search criteria use the Logical Condition Association text box to specify the Boolean operator AND or OR that will be used between criteria See Figure 3 55 e AND operator Only the records that meet both criteria will be returned e OR operator Records meeting either search criteria will be returned The field below the radio buttons displays the combined query that will be run against the database For ex
214. namic License Server Connection dialog box This opens the Internet Settings dialog box where you can alter your proxy settings Figure A 8 Internet settings for trial license ORE EA GZ Use Internet Explorer settings Direct connection Cancel Use proxy server Proxy server Port E I Ergen requires authentication User Password Tx Figure A 8 Internet Settings dialog box The Internet Settings dialog box allows you to set your connection parameters If the Use Inter net Explorer settings button is selected License Manager will attempt to make the connection using your default settings If default detection is not successful you can either choose the 188 License Manager Appendix A Direct connection button if you do not have a proxy or choose the Use proxy server button and specify the proxy name port and password information Press the OK button to return to the Dynamic License Server Connection Tester dialog box 189 Vector PathBlazer 2 0 User s Manual 190 APPENDIX DTD FOR DATA IMPORT This appendix includes the Document Type Definition DTD for mapping proprietary data to a PathBlazer formatted XML file for import lt ELEMENT storage list_of substances list_of_interactions gt lt ATTLIST storage ID ID REQUIRED gt lt ELEMENT list_of_substances substance gt lt ELEMENT substance list_of_origin _accesses creator create_date update_date list_of_hyperlin
215. nd press the Find button Click on the result in the left panel the term will be simultaneously highlighted in the GO tree on the right Click the Add button 61 Vector PathBlazer 2 0 User s Manual The GO term displays as a condition in the Search Pathways Create Subset dialog box Figure 3 61 Search Pathways Create Subset Ez E x Search Conditions C1 GO Annotation apoptosis inhibitor activity G0 0008189 E Add Single Condition Add Multiple Condition Edit Delete Logical Condition Association f Or And Custom Search In Subset JO Demo Pathways a O Fall Metabolic Pathways Si Signaling Pathways E i oS d Back Hent gt Close Help Figure 3 61 The Search lt Object gt Create Subset dialog box displaying a GO annotation search condition In the Search in Subset panel check one or more subsets to be searched for objects annotated with the GO terms you have set as conditions Click the Next button Search Pathways Create Subset E EA Search Results a Glycolpsi Glpcolysis Pathway discov Glucaneagenesis Pathway Gluconeogenesis Pathway 2 items have been found Append selected items to subset Save the search results as a subset Hentz Close Help Figure 3 62 Database search results display objects that contain GO annotations used as search conditions Search results display in the Search Pathways Create Subset dialog b
216. nded to provide data for extracting information about protein interactions and interaction networks in biological processes 1 A complete description of the contents of the DIP database as well as licensing information is available at http dip doe mbi ucla edu hold Reference and licensing information is also avail able in Appendix C DIP Source Files and Import Logic The file dip YYYMMDD xin is used to load DIP data into the Vector PathBlazer database where YYYYMMDD is the date of a database release for example dip20020616 xin Download this file from http dip doe mbi ucla edu dip Download cgi The file consists of two parts components and reactions A component object is created for each component listed in the file The following is a partial example of the part of the file that contains component information Values of attributes or elements that are directly parsed are in bold XML Source lt node uid DIP 3N id 3 name RA52_YEAST class protein gt lt att name organism gt lt val gt Saccharomyces cerevisiae budding yeast lt val gt lt att gt lt node gt 1 http dip doe mbi ucla edu hold 97 Vector PathBlazer 2 0 User s Manual 98 The following table shows the XML tag that is parsed from the component part a description of its value and where the value displays in the program Table 4 5 Description Annotation d in Vector PathBlazer lt node name gt Recommended name Componen
217. ne number and email address in the appropriate fields Note If you already entered your personal information on the Personal tab it should appear here when you open this dialog box Enter the server URL or click the Default URL button to enter it automatically Press the Internet Connection Settings button to configure your connection settings and to enter server proxy information if a firewall is used at your site See the Internet Connection Sett tings section on page 188 for more information For information on the Test Connection button see page 188 Important Trial licenses are served from Invitrogen To receive your trial license send the Hardware ID from the Trial License dialog box to trial informaxinc com with your personal information You will generally receive a prompt reply usually within one business day Once you have received the reply testing the connection see following section will show that licenses are available 187 Vector PathBlazer 2 0 User s Manual Once you have tested the connection and have a Trial License available the Set for All Appli cations button becomes available Click this button to set all Vector applications applications to Trial Licenses Once you do this when you close this dialog box the Applications tab now shows Trial License for all applications Note When you set Trial Licenses for all applications this operation only applies for those applica tions for which you do not have
218. ned on it is printed and or exported in the image file A small graphic display in the format of a bar diagram with colors coded from the expression col ors palette can display as a label next to a component in the Graphics Pane These small graphs are designed to give you a quick grasp of expression differences Figure 8 18 The Y axis of these graphs are expressed in relative units rather than actual expression values To show hide these graphs select View gt Show Hide All Expression Difference Labels 3 1 1 Z 3 EA Glycolysis Pathway Discovery unrestricted view Database Glucose EO Expression Palette Fructose 6 phosphate 4 Master View Figure 8 18 Small bar graphs representing expression values circled can display next to their corresponding components in the Graphics window The Expression Palette displays to the upper right of the Graphics window Displayed expression graphs are printed with the Graphics window and or copied and exported with image files The following figure shows glycolysis displayed in Discovery View Figure 8 19 In Discovery View the colors assigned to the expression values ranges are associated with the actual com ponent the enzymes in this example In Metabolic View the enzymes in the pathway display with the reaction nodes and the expression values display on the reaction nodes 179 Vector PathBlazer 2 0 User s Manual EES vector PathBlazer 2
219. nes use this button for linking genes with no known corresponding components in PathBlazer This option leaves the rest of the template intact Click one of the following buttons to choose the basis for the links Using DB Links uses links to an external database to do the mapping For exam ple a gene has a link to GB entry A1 1234 a protein in PathBlazer has a link to the same GenBank entry The gene and the protein will be matched in the template Using Names and Synonyms uses names and synonyms to the the mapping For example a gene is named Top 1 a component in PathBlazer is named topoisomerase and has a synonym Top 1 They will be matched e Relink All Genes use this button to recreate links for all genes and components as they were previously mapped This operation creates links that are different than those that existed before Using DB Links see above bullets Using Names and Synonyms see above bullets Click Next The next screen allows you to specify an import name and to save the component to gene name ID map as a template The Import name is the name associated with the set of expression values contained in the currently selected expression data file The template name is the name associated with the linked association table of gene names to component names In the Import Name field enter a name for the expression data values If you want 173 Vector PathBlazer 2 0 User s Manual to save the ma
220. ngle database and use the data together to discover novel pathways and networks At any time you can select a new database and view the contents of that database You can also share individual pathway data by exchanging path way files pw files with colleagues who also have Vector PathBlazer For more information about pw files see Saving a pw File to the Database on page 51 Create a new database by selecting Tools gt Manage Databases gt Create New Database In the dialog box that opens enter a name for the database file and navigate to the location where you want to save the file You can save it to the Vector PathBlazer installation directory or any other directory Click Save The new database file is created and the path to the file displays as a submenu when you select Tools gt Manage Databases The newly created database has a minimal set of important molecules until data is imported into it or created in it Choose a database for use by selecting Tools gt Manage Databases gt Select Database In the dialog box that opens navigate to the location of the database file that is the mdb file you want to use and click Open One database at a time can be viewed in Vector PathBlazer The paths to recently opened databases display as submenus when you select Tools gt Manage Working with Pathways Chapter 3 Databases For example the default database that initially opens when you launch the program may display on the desktop
221. nment Aligns clusters with other clusters Alignment tool centers tops or bottoms Table 3 1 Settings for Circular layout 25 Vector PathBlazer 2 0 User s Manual Hierarchical Tab The Hierarchical layout settings display in Figure 3 23 and are described in Table 3 2 Layout Properties E E 3 Z EO Circular GO Hierarchical gf Symmetric Incremental Layout Respect Flow Spacing ld Variable Level Spacing Orientation C Left To Right Bottom To Top Right To Left Gz Top To Bottom Ge Proportional Spacing I Reduce Crossings ZI Constant Spacing Between Levels jo Between Modes li 00 kd Minimum Slope GO Layout Quality Draft Default C a Cancel Layout Reset Defaults Help Figure 3 23 Settings for Hierarchical Layout Orientation Right to left and top to bottom orienta tion of the image Right Spacing Variable Level Spacing Changes the positioning of levels according to the density of edges between levels Connectors Routing Orthogonal Routing la Calculated Sizes Horizontal Spacing IE Vertical Spacing IE Level Alignment Center Top Bottom I Undirected Layout Proportional Spacing Creates space around nodes that is proportional to the node size Constant Spacing Creates space around nodes that is the same for all nodes Values Between Levels Between Nodes Minimum Slope Checked On Defines the tangent
222. nnotations display at the bottom of this dialog box e Click the Choose Color button In the color box that opens select the color for the spec ified GO display This selection reveals itself in the following way When a color is applied to a GO term and the same GO term is associated with a database component the component displayed in the Graphic Pane exhibits the customized color Figure 3 20 e Select the Hide radio button to hide all of the specified GO annotations When you click the Hide button a second time hidden objects display Once a term and its suboptions are selected click the Add button The term is added as a con dition to the Filtering Highlighting dialog box If you select the condition then click the Edit but ton you are returned to the Add GO Condition dialog box where you can modify your selection You can also delete the condition by selecting it then clicking the Delete button 23 Vector PathBlazer 2 0 User s Manual 24 e Click the Apply button to execute the filtering highlighting conditions you have just defined See Figure 3 20 to note how a color applied to a GO annotation is implemented ES Glycolysis Pathway Discovery unrestricted view Database Figure 3 20 When a color is assigned to a GO term that applies to an object in the Graphics window that object exhibits the color View and modify a graph s properties by clicking anywhere except on an object in the Graphics window an
223. not applied to the new unnamed reaction This is the only option available when an unnamed component is added to a reaction Table 5 3 Options when a component is added or a connector is changed in a reaction Adding a Component to a Saved Reaction To add a new component to a reaction that has already been saved to the database use the fol lowing steps 1 Add a component by selecting a shape from the Palette window or dragging a component from the Database Explorer Connect it to a reaction node with a line from the Palette win dow to form a connector between the new component and the reaction node When a con nector links the newly added component to the reaction node the dialog box described in the next step automatically opens The actions available in the dialog box depend on whether a component is named or unnamed in the Graphics window 2 Ifthe added component is unnamed that is a name has not yet been assigned to a newly drawn shape in the Graphics window the dialog box in Figure 5 24 displays with only one available option in the Action box Disconnect the reaction from the pathway 128 Note Drawing Pathways Chapter 5 Disconnect refers to the current reaction because in order for a component to be added to a saved reaction the component must be named Therefore an unnamed reaction takes the place of the original reaction ector PathBlazer ie ae Be EA fou are about to add a component to reacti
224. ns Figure 4 15 x PathBlazer Import Select import module POD Import Biolyc Formated data User PPI Import User PFI data Import DIF data pe import KEGG v 26 data Trans lronort TransPath data KA Descriptions b data from DIP database lt Back Cancel Help Figure 4 15 DIP file selected for import 3 Shoose Import DIP Data The Description box reflects the type of data chosen for import Click Next 99 Vector PathBlazer 2 0 User s Manual 4 In Screen 2 of the Import Wizard select the DIP xml file for import by clicking the Browse button locating the corresponding file in the Open dialog box and clicking Open The com plete path to the file displays in the Select source file field Figure 4 10 Click Next to con tinue PathBlazer Import E z Select source file E ARI TADU tles ro2all db rd lt Back Next gt Cancel Help Figure 4 16 Dip Import dialog box for selecting the DIP source file 5 In the Merge Options dialog box select the options appropriate for merging the data See Merge Option Dialog Box on page 67 for more information Click Next to continue The data loads while a monitor displays allowing you to follow the import process An import log summarizing import results displays when the import has been successfully com plete displays the progress of the import 6 To stop the import click Cancel Click Close Once imported verify the import pro
225. nse type Unregister in the License Number field and click Apply You will be warned that you are trying to reset your static license and asked if you want to continue If you answer Yes the application will reset your license and will send proof of this operation to the Invitrogen server If the connection to the server fails you will receive notice of this Dynamic License Dialog Box Note To configure your Dynamic license click the Dynamic button at the bottom of the Applications tab Figure A 3 This opens the Dynamic License dialog box Figure AOK i E W x Dynamic License Organization DotCom Phone number 240 846 3398 E mail address L browm dotoom com URL of DLS DLS server requires authentication Hame Password Internet Connection Settings Set for all applications Test Connection Apply Cancel Figure A 5 Dynamic License dialog box Enter your name organization phone number and email address in the appropriate fields This sets the user information in Vector PathBlazer If you already entered your personal information on the Personal tab it should appear here when you open this dialog box License Manager Appendix A In the URL of DLS text box enter the DLS server URL supplied by the DLS administrator at your site If your DLS server requires a password make sure the authentication settings are filled in appropriately Press the Internet Connection Settings button to conf
226. o lt bidirect gt lt type gt ordinary lt type gt lt weight gt 1 lt weight gt lt conf_arc gt lt BioNet gt lt pathway gt lt list_of_pathways gt Instructions for Importing Proprietary Data You can import data either into the default PathBlazer database or into a new separate database you create before the data import To create a database see Creating a New Database on page 10 You must also have formatted proprietary data according in Vector PathBlazer XML file format described above The complete DTD is included in Appendix B 105 Vector PathBlazer 2 0 User s Manual Use the following steps to import proprietary data into the Vector PathBlazer database 1 Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 2 From an open PathBlazer window select File gt Import The PathBlazer Import tool opens displaying the various import options Figure 4 79 paar S dr rd x PathBlazer Import Select import module gg Import KEGG v 26 data Ile Import TransPath data Import of data from ML file BIND Import BIND data Descriptions mport of data from ML file Description lt Back Cancel Help Figure 4 19 XML file selected for import 3 Inthe Select Import Module box choose Import of data from XML file The Description box reflects the type of data chosen for import Click Next 4 In Screen 2 of the Import Wiz
227. oads while a monitor displays allowing you to fol low the import process An import log summarizing import results displays when the import has been successfully complete To stop the import click Cancel A message displays when the import is complete Click Close Once imported verify the import process by choosing an example of a KEGG reaction in the Graphics window Reaction directionality is explicit in the KEGG database v 22 and later If the reaction is bi directional it is stored as two reactions in PathBlazer Importing BIND Data 80 BIND Biomolecular Interaction Network Database stores full descriptions of interactions molecular complexes and pathways Development of the BIND 2 0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins nucleic acids and small molecules Chemical reactions photochemical activation and conformational changes can also be described The Importing Data Chapter 4 database can be used to study networks of interactions to map pathways across taxonomic branches and to generate information for kinetic simulations A complete description of the contents of the BIND database as well as licensing information is available at hitp Awww binddb org Reference and licensing information is also available in Appendix C BIND Source Files Three main data types are defined in the BIND databas
228. of any kind and Invitrogen will not be liable for any damages This version of the Vector PathBlazer 2 0 User s Manual was published in March 2004 Invitrogen InforMax Technical Support USA Phone 240 379 4240 800 357 3114 Toll free U S E mail techsupport informaxinc com Europe Middle East Africa Asian Pacific Phone 44 0 141 814 6350 E mail euroinformax invitrogen com TABLE OF CONTENTS Chapter 1 Introduction to Vector PathBlazer saso 1 Chapter 2 Overview of Vector PathBlazer assa 5 Chapter 3 VVOFKING WIIN PatnWayS errateaz bek e Ea a beek raketa 9 Chapter 4 IMPON Ker GA 65 Chapter 5 Drawing SSL EA AAA 109 Chapter 6 Automatically Assembling Pathways cccccsseeeseeceeeeeeeeeeseeeeeeeesees 133 Chapter 7 GENE elaia Ua 153 Chapter 8 Working with Gene Expression Data cccccseceeeeeseeeeeeeeeeeeeeeeeeseeeeeaees 165 Appendix A License Managel dA 183 Appendix B DTO FOF Data IMPONE scivia aaa 191 Appendix C Gue dl aea 199 Appendix D de eiz lala diala KAE 203 EU Erla 209 MOOK raan 211 Vector PathBlazer User s Manual Table of Contents Chapter 1 introduction to Vector PathBlazer AAN 1 LS gts eee eae EO l Getting Started with Vector NTI PathBlazer sa l Manual baia 2 SRU Sasien aA 2 DV SCSI TR COUT CIVIC gi 2 Wsing Online Help aaa ect aak Abeba 3 Contacting Egea Seui SR 3 Conventions Used in this Manual sua 4 Chapter 2 Overview of Vector PathBlazer assa 5 ar
229. og box that opens Figure 5 2 Click Add enter its name in the dialog box and click OK The component is added to the list Set Expression Data Ranges Set Palette Pull Down Molecules Molecule o O H20 NADP NADPH NAD NADH Orthophosphate Coe ADP Edit Delete OF Cancel Help Figure 5 2 Tab in the Options dialog box where components are added to the common molecules list Edit the name of a component in the list by selecting the component clicking Edit and changing the name Only primary names of components in the database and not synonyms can be added to the Common Molecules list If the component added to the list is not already present in the data base you will be able to add it to the list but you will receive an error when you try to draw the component in the Graphics window Add it to the database by importing it or by drawing it in the Graphics window and saving it to the database The same is true if you edit the name of a com ponent to one that is not present in the database Delete a component from the list by clicking Delete The component is removed from the list only it is not removed from the database Drawing a New Pathway 112 There are several ways to draw new pathways in Vector PathBlazer Use the steps outlined in the following sections to draw a new pathway Opening A New Graphics Window Use the following steps to open a new Graphics window 1 Select File gt New
230. ology Terms on page 154 2 Manually annotate 3 components that are part of the glycolysis pathway as described in steps 3 7 3 From the All Pathways folder in the Database Explorer open the Glycolysis discovery pathway 4 From the Graphics window for each component listed in the Component column of Table 7 7 open the shortcut menu and select Component Properties 5 On the Component Crosslinks tab click Add 162 6 10 Gene Ontologies Chapter 7 In the Crosslink tab accept Database for the Type Option In the Database field enter SwissProt For each of the components enter the Accession ID displayed in Table 7 1 This enters links to the SwissProt database for these objects When you import gene anno tations crosslinks in that file to the SwissProt accession IDs you have just entered for these objects will automatically add GO annotations to these database objects Phosphofructoki SwissProt P09237 nase Table 7 1 Selections for manually assigning GO annotations to selected glycolysis reaction components For each entry click OK returning you to the Properties dialog box Note that the GO tab for each is still empty Import the Gene Annotations file sptr goa as described in mporting Gene Ontology Annota tions on page 159 The results should tell you that 27 annotations are imported After the import open the Component Properties dialog boxes again to these three objects Note the GO annotations on the GO
231. on OK already existing in the Database Please select action to take rr e Cancel i Updetereacton f Create new reaction _ Disconnect this reaction from pathway GE Reaction Name glycolisis mene SEE d GIRO E ge Component Name lt UNNAMED gt IEE seer at Component NOTE In order to add component to a reaction you have to name it frst Figure 5 24 Option when adding an unnamed component to a saved pathway The original reaction name for example glycolysis _rxn2 displays in the Reaction Name field and the Component name lt UNNAMED gt displays in the Component Name field To disconnect the reaction from the pathway click OK Since a reaction saved to the database cannot contain any unnamed components the original reaction is disconnected from the pathway and a new reaction called lt UNNAMED gt that contains the newly added connector and lt UNNAMED gt compo nent is added in its place Additionally lt UNNAMED gt reactions cannot be saved to the database The reaction that now displays in the Graphics window is the lt UNNAMED gt reaction The original reaction glycolysis _rxn2 in this example remains unchanged in the database but is no longer connected to the pathway To name the component from the dialog box click Component and name the component by following the instructions in either Drawing a New Component on page 113 or Drawing an Existing Component on page 118 Once a component is named
232. on For example ENTRY R00093 NAME L Glutamate NAD oxidoreductase transaminating DEFINITION 2 L Glutamate NAD lt gt L Glutamine 2 Oxoglutarate NADH will be named L Glutamate NAD oxidoreductase transaminating and have the formula 2 L Glutamate NAD lt gt L Glutamine 2 Oxoglutarate NADH KEGG Genome File The Genome file contains information about completely sequenced organisms This file is used by the Vector PathBlazer importer to assign a species to the three letter species codes listed in the Gene field in the Enzyme file For example in the partial example of the Enzyme file shown 78 Importing Data Chapter 4 in the KEGG Enzyme File on page 75 the GENES field contains the entry HSA 124 ADH1A HSA in the GENES field of the Enzyme file is matched to the corresponding value in the ENTRY field in the Genome file The species is then determined by assigning the value in the DEFINITION field in the Genome file to the Organism attribute in Vector PathBlazer In this example the spe cies is identified as Homo sapiens A partial example of the Genome file as it appears in a text editor follows The fields that are referenced are in bold ENTRY hsa NAME H sapiens DEFINITION Homo sapiens TAXONOMY TAX 9606 LINEAGE Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Euth eria Primates Catarrhini Hominidae Homo III Instructions for Importing KEGG You can import data eithe
233. on components 178 gene ontology annotations 22 Palette window 12 status bar 11 Document Type Description see DTD 191 Drawing existing component in Graphics window 118 121 existing reaction in Graphics window 125 new component in Graphics window 113 new reaction in Graphics window 122 opening Graphics window 112 pathway in Discovery View 109 pathway in Metabolic View 109 tools 110 DTD importing proprietary datain XML format 191 Dynamic License 183 E Editing expression template 170 GO annotations 159 Experiments definition 7 Expression data Annotation field 44 assigning display colors to value ranges 179 bar graph values 179 creating template for import 166 displaying values on pathway components 178 importing with template 168 introduction 165 linking to pathway components 166 mapping database links manually 171 modifying expression value colors 179 sending to PathBlazer from Vector Xpression 177 Expression Palette 179 F Filtering schema creating 21 hiding 21 Folders adding subfolders and subsets 34 creating 34 deleting 34 Font changing in Graphics window 20 21 G Gene expression See Expression data 165 Gene ontologies annotating objects 157 annotation field 43 downloading files 153 examples 162 importing 153 importing annotations 159 Gene Ontology customizing display 22 deleting a GO annotation 159 editing a GO annotation 159 importing GO annotations 159 importing GO terms 154 introduction 153 linking
234. on direction 126 Drawing Pathways Chapter 5 To see more details about a reaction slide the divider bars of any column to the left or right to make a column larger or select a reaction and select Properties from the shortcut menu select one or more reactions to add to the Graphics window by selecting the checkbox next to each reaction in the Reaction column and click OK Figure 5 22 Add Reaction Matching Reactions Reaction Formula CI gluco pri glucolysis_ mend Glucose 6 phosphate Fr C pentose_rn3 C pentose_rn7 Show Aeachons with Generality R OO EZ rr pale E Figure 5 22 List of reactions returned that match a selected component by primary name and direction 5 The reaction is added to the pathway by joining it to the selected component Figure 5 23 EE re New PathWay 1 Discovery unrestricted view Database E Glucose reaction 1 Enzyme Protein EE selected Undefined naemed rb Hexokinase 2g component e H20 GEk TUTO T Glucose phosphate Fructose 6 phosphate Ae oe i EA Interaction d E Glucose 6 phosphate isomerase reaction 2 Catalysis oe Activation a e o Ii Master View Figure 5 23 Reactions joined by a selected component Changing a Saved Reaction To store a reaction in a pathway and save it as an independent object the reaction must be saved to the database When a reaction is saved associations to the connectors and compo
235. onent dirutu PS zal re Figure 5 14 Component wizard with Database Component selected 7 The remaining screens in the Component wizard are for adding annotations to a compo nent which may or may not already be annotated If you do not want to add annotations click Next in each screen until the Finish button displays in the last screen Click Finish to name the component in the Graphics window The Annotation screens are the same as those described in step 4 on page 115 through step 8 on page 117 For a description of each annotation field and its values see Annotating Pathways Components Experiments Reactions and Connectors on page 37 8 When you have finished adding annotations the component is named in the Graphics win dow based on the selected component Figure 5 15 Any annotations that were changed are also saved to the database To change the graphical properties of a component for 120 Drawing Pathways Chapter 5 example font color and size see View and modify an object s graphical properties on page 19 EE vector PathBlazer 2 New PathWay 1 File Edit view Tools Layout Window Help are l x E F E e x La Expression Data Sets None Expression Runs E EEE EZE a SP ZIA GIZZ A ze New PathWay 1 Discovery unrestricted view Database A lt Physical Lipid DNA RNA Enzyme Glucose Protein Undefined i H20 Normal Interaction v _
236. onent aaa 141 Building a Pathway from a Starting Pathway to an Ending Component raa 143 Building a Pathway Through a Component rra 145 GANERRA EEE aua a A ataka 147 Building A Link Between Two Pathways rss 149 Showing Connections to Data from Other Datasources rra 150 Chapter 7 Gene Ontologies saiisine a a 153 Introduction to Gene Ontologies raa 153 Vector PathBlazer User s Manual vi W orkine with Gene Ontology HEE 154 Tapori Gene Ontology eau AAA 154 Viewing Gene Ontology Bean EAE 155 Searching Gene SIG TEMS asin a E ie aula ule 156 Manual Annotation of PathBlazer Objects with GO Terms rra IEE KORTE abeak aiak atate baaa azieta aate 159 Working with Gene Ontology Annotations rss 159 Importing Gene Ontology Annotations rss 159 Population of Organism Subcellular Location Attributes Based on GO Annotations 161 Sample Workflow Using Gene Annotations rrura 162 Chapter 8 Working with Gene Expression Dt sssssza seas 165 Introduction to Expression Data Import and Display a 165 Interaction Between Vector PathBlazer 2 0 and Vector Xpression 3 1 166 Linking Gene Expression Data to Pathway Components rra 166 Creating an Template Automatically AAE 166 Importing Expression Data with a Template ss 168 Bie HOS bera aea 170 porine a Template EE 171 Mapping Database Links Manually rrua 171 Creating a Tab Delimited Data File of Expression Values cceesseeseeeeeees 174 Exchanging Data Between Vector
237. onents or reactions to a pathway see Adding a Component on page 113 Annotating Pathways Components Experiments Reactions and Connectors An annotation in Vector PathBlazer is a property or an attribute that can be added to an object Annotations can be useful for recording pertinent information about an object or for searching for objects in the database that all have a property in common For example a search of Epider mal Growth Factor EGF on OMIM hitp www ncbi nim nih gov entrez dispo mim cgi id 131530 displays a summary of what is currently Known about EGF it has a role in growth control and has been implicated in malignant melanoma In addition to the interactions EGF makes with other known proteins namely the EGF receptor which mediates a cascade of signal transduction events that can be stored in the Vector PathBlazer database each of these known properties can be included as annotations to EGF When objects are imported into the database many annotations are automatically imported with the objects For more information about importing data see Chapter 4 Each object type in Vector PathBlazer including pathways components experiments reac tions and connectors has a specific set of fields that can be associated with a particular object type Some fields have a pre defined set of values and other fields accept other formats such as text strings and numbers Annotations can be added to an object during several different
238. ons you made in each Create a new Alternate View from any tab including the Text View tab or another Alternate View tab by selecting Tools gt Manage Alternate Views gt Create View Name the view in the dialog box that opens and click OK A new tab is added to the Graphics window either next to the Text tab or next to the last Alternate View tab that was added If you modified the display of the graphical elements in the Master View as in Figure 3 28 where common components are given similar shading and text styles the graphical properties are removed in the new Alternate View and the default graphical properties display as in Figure 3 29 To save the new view to the pathway click Save For more information see Saving PathBlazer Components Reactions and Pathways on page 46 RE ector PathBlazer 2 Glycolysis Pathway Fie Edit view Tools Layout Window Help in Expression Data Sets None Expression Runs A Jz ula S S eee Es Glycolysis Pathway Discovery unrestricted view Database SD aw 58 D ZO aa GO w Fructose 6 phe i gt D T a EE Glucose 6 phosphate Glucose ila 3 E 4 Figure 3 28 Modified graphical properties in the Master View HE ector PathBlazer 2 Glycolysis Pathway E O xl File Edit View Tools Layout Window Help ba e X IA gl Expression Data Sets None Expression Runs Si b Ni A
239. open discovery pathway to display with a yellow background Select Tools gt Filtering Highlighting gt New Filtering Highlighting Schema In the Add Condition dialog box that opens select Add Component In the Add Con dition dialog box select Component Class in the Condition Type drop down menu In the Component Class drop down list select Protein In the Protein Subclass drop down menu select Enzyme You can enter the EC Number Enzyme Classification and Generic Name in the appropriate text boxes but they can be left blank Click the Choose Color button and select yellow from the color palette Click OK then click Add That returns you to the Add Con dition dialog box where you see the new condition you have just configured Figure 3 78 Filtering Highlighting Condition Default Color Class Protein Enzyme Figure 3 18 The Filtering Highlighting dialog box displays new conditions for universal display Click Apply to apply the schema to all of the displayed enzymes To edit any of the conditions listed including the Default Color select it and click the Edit button To save a schema select it and click Save Name the schema Once a schema is saved it will be listed in the Add Condi tions dialog box when you open it Later you can apply a schema you have saved to any speci fied objects using the Filtering Highlighting feature Customize gene ontology display by selecting Tools gt Filtering Highlighting gt N
240. or seats with the number of users at any one time being limited to the number of licenses specified in the contract e Trial License Allotted to a potential purchaser of Vector software for a specified number of days during which the user can review and use the software within certain limits e Demo Mode For the purposes of demonstrating the Vector software Some functionality is disabled in Demo Mode When you open the Vector PathBlazer software a checkmark icon such as this UTZ at the bottom right corner on the Status Bar shows the current license status Pause the cursor arrow over the button and a pop up label displays the license status e Green checkmark active Static License e Green blinking checkmark active Trial or Dynamic License e Red blinking X the application is not licensed running in Demo mode License Manager does not open automatically when you install Vector PathBlazer or Vector Advance on your computer You must open License Manager manually To open License Man ager select it from the Start menu Start gt Programs gt InforMax 2003 gt Vector PathBlazer 2 gt License Manager or click Help gt License in the PathBlazer Viewer once you have opened it 183 Vector PathBlazer 2 0 User s Manual License Manager Dialog Box The License Manager has three tabs the Contact Us tab the Personal tab and the Applica tions tab Contact Us Tab The License Manager opens by default to
241. or PathBlazer 2 0 User s Manual Launching PathBlazer Viewer To launch the PathBlazer Viewer select Start gt Programs gt InforMax 2003 gt Vector Path Blazer 2 gt PathBlazer 2 from your computer s start menu PathBlazer Viewer opens and ini tially displays a blank screen with unavailable toolbars until you open a pathway Figure 3 7 E83 ector PathBlazer 2 EISE File Edit Yiew Tools Layout Window Help A X EZ bel PK a S Expression Data Sets None E Expression Runs IK ZZ SZ dT OTS amp e Sare SiiS Z U A D S d eiz d Components Folder J Reactions Reactions Folder Pathways Pathway Folder E Experiments Experiments Folder Folder PathBlazer Database C Documents and Settingsijill INFORMAXINC My Documents My PathBlazer DatalPathBlazer PathBlazer_dem JE a Figure 3 1 PathBlazer Viewer displays a blank screen on initial launch Creating a New Database 10 Since Vector PathBlazer is designed for a single user there are no permission or user identifica tion schemes All data is visible to any user who starts the program on the computer where it is installed You can partition individual user data data sets projects experiments etc into differ ent databases by creating new databases that is new mbd files for any of these purposes However one of the key features of Vector PathBlazer is the ability to import data from several public sources as well as proprietary data into a si
242. ore using one of the methods described in Adding a Component on page 113 To add a connector between two components to create a reaction select a line from the Pal ette window and move the cursor to the Graphics window where it changes to a wand E Click on the first component you want to link drag the wand to the second compo nent and click on the second component Continue to the next Drawing Pathways Chapter 5 The connector is drawn between the two components Figure 5 17 Once two components are linked a reaction is formed between the two and is represented by a reaction node A ESS vector PathBlazer 2 New PathWay 1 i ZIZ E File Edit view Tools Layout Window Help A bd r EE Lei Pas Lad Expression Data Sets None Expression Runs Iroa Ra X oleja or TAB ZOA Glz Bw h a Ee EE New PathWay 1 Discovery unrestricted view Database SS mle oj EA Physical lt gt ipid Glucose gt DNA RNA ZE Enzyme EE Protein E Undefined BEE H20 Glucose 6 phosphate rk Normal 4 gt Interaction Master View I e gt alae X Zoe S ES EZTI kN TE E UA PathBlazer Databas Name 3 astasource Description Formulas Gate al ERE Components du GLUCOSAMINE 1P Mol weight 259 152 SMI C6H14NO08P 1 9 2004 9 23 43 4M fa All Compone diu glucosamine 6 phosphate deaminase Catalyzes H2O D gluco 1 9 2004 9 23 32 4M SI CL molecule
243. ot Known if it is in the ER In Vector PathBlazer values are set to lt Nucleus 0 gt and lt ER no value gt Both a strict and a non strict search for lt Location Nucleus gt do not return ERBA A strict search for lt Location ER gt also does not return ERBA However a non strict search for lt Location ER gt does return ERBA In the Add Multiple Condition dialog box select the Condition Type from the drop down menu Figure 3 54 Add Condition E E Condition Type PathwayName sss Name ATP ADP H20 Add From File Add Cancel Help Figure 3 54 The Add Condition dialog box for adding multiple conditions for a database search In the large text box add any number of multiple conditions in one of several ways Type the multiple conditions in list format o Click the Add from File button to locate a text file with the search conditions listed Click the Add from Subset button to locate an existing subset containing the objects you want to list as conditions When you choose the subset then click Select all of the objects in the subset will display in the Add Condition dialog box When you have finished configuring the search condition s click Add The search condi tions are added to the Search lt object gt Create lt object gt dialog box with a condition identifier of C1 next to it For a single condition the identifier is specified For multiple conditions C lt gt Name List Conditio
244. ot be accessed from the graphic view in a metabolic pathway e In a Discovery pathway enzymes are represented as oval shapes connected by arrows to the open pathway Properties for the enzymes can be accessed from the short cut menu associated with the displayed components Components are linked to reactions by connectors which are represented as single or double headed arrows or straight lines Generally reactions are represented as circles or reaction nodes and are linked by connectors to the components that are included in a particular reaction Two kinds of reactions can be represented in Vector PathBlazer directed reactions and protein protein interactions A directed reaction can be represented unidirectionally that is forward or reverse or bidirectionally that is forward and reverse as lines with single or double headed arrows The direction of an arrow indicates how a component contributes to a reaction How Working with Pathways Chapter 3 ever a directed reaction does not necessarily have to end in a product Several examples of directed reactions are shown in Figure 3 5 and Figure 3 6 Mol A Mol A Mol amp Mol B Figure 3 5 Mol A interacts with Mol B Figure 3 5 Mol A interacts with Mol B ina both are Components in a forward forward direction to form a complex direction the reaction is represented by a circle with no known product s A protein protein interaction involves two proteins interacting without a reactio
245. otation 41 opening from Graphics window 52 Customizing column display in Database Explorer 32 gene ontology display 22 graphical layouts 24 graphical properties 19 universal color schemes for objects 21 D Database mdb file 6 backing up 11 creating 10 default installation 6 description 6 main data types 6 pre loaded data 7 selecting mdb file for use 10 updating from PathBlazer 1 0 11 Database Explorer adding components reactions pathways to Graphics window 36 browsing data 31 building pathways 139 changing column display 32 Contents Pane 13 creating folders 34 creating subsets 34 description 12 hiding 13 List Pane 13 moving 13 organizing data 33 reversing reaction direction 35 searching database 54 Database search multiple conditions 54 single condition 54 212 Data Import See Importing 66 Data types component 6 pathway 7 reaction 6 Deleting Alternate View 31 annotations 116 component from saved reaction 130 components from commonly used molecules list 112 connectors 131 folders 34 labels 132 objects 33 subsets 35 Demo Mode 183 description 14 DIP data display 100 description 97 import instructions 99 import logic 97 source files 97 Direction connector annotation 45 in pathway building 137 ofa reaction 7 14 reversing for reaction 35 Discovery View building a pathway 138 description 14 109 opening new Graphics window 112 Displaying Database Explorer 13 expression values
246. otein protein interactions if non directed components is chosen is set to the level used to generate the original pathway If no interaction generality score was set for the original pathway the default value is infinite thereby showing all possible interactions Building Pathways by Selecting Reactions in the Database Explorer Pathways can also be built by selecting two or more reactions in the Database Explorer When pathways are built this way the program attempts to link common components from the selected reactions into a network or pathway Discovery View is the default display view and components are pooled In addition there is no way to select a from or to component To build a pathway from reactions selected in Database Explorer use the following steps 1 Select two or more reactions in the List Pane and select Build a Pathway from the shortcut menu 2 The resulting network or pathway displays in the Graphics window Examples of Automatically Assembling Pathways The following examples show the pathways that are automatically assembled when certain parameters are selected Each example is illustrated using components and reactions from the metabolic pathway glycolysis to show how the algorithm assembles a pathway in the context of a well known pathway The reactions include the steps of glycolysis and all the components involved in the reactions including the small molecules like ATP etc Each example shows the input co
247. ou are creating the template Working with Gene Expression Data Chapter 8 automatically you probably will have no need to perform any edits in this dialog box how ever for detailed directions about using this dialog box see step 2 through step 5 begin ning on page 172 Click Next Pathway Components Ed Expression Data Component Gene Hexokinase HXK1 Glucose 6 p PGN Phosphofruc EEK Aldolase EEA Triose phos TPI Glyceraldeh TDH1 Phosphoqly PGK1 jal AL Jr hse Link Orphan Genes Relink All Genes Using DB Links Using Names and Synonyms Using DB Links Using Names and Synonyms Back Cancel Help Figure 8 4 Map screen In the Specify an Import Name screen name the expression data file in the Import Name field Figure 8 5 This will be the name that displays for the selected data set in the Expres sion Data Sets drop down list Specify an Import Name a x Import Name Upregulated Import Subset lt Back Cancel Help Figure 8 5 Naming the expression data set In the Import Subset field use the drop down menu to select the subset into which the expression data is to be placed upon import Click Next The Destination Pathways screen is for associating the expression values defined by the current expression file with one or more pathways that contain components included in the 169 Vector Pa
248. ox Figure 3 62 Click the Back button to return to modify conditions and re initiate the search View the properties of any object by first selecting it and then selecting Properties from the shortcut menu The Properties dialog box opens where you can review or change any of the object s properties To create a subset from the results select one or more of the result objects and click on of the following buttons 62 Working with Pathways Chapter 3 Append Selected Items to Subset to save the results as part of an existing database Select the items you want to save and click the button In the Append to Subset dialog box select the subset to store the selected search results and click Append Save the Search Results as a Subset to create a new subset containing search results In the Create Subset dialog box name and describe the new subset in the appropriate text boxes Click the Create button This creates a new recipient subset containing all search results and closes the dialog box Printing and Saving Images Publication ready images can be printed directly from Vector PathBlazer to a local printer Images can also be saved or copied to the local file system in several common formats which you can then manipulate using other graphics programs or open in word processing programs Printing an Image Only the contents of the Graphics window can be printed This includes the contents of the Mas ter View an Alternate View o
249. p www genome ad jp kegg Reference and licensing information is also avail able in Appendix C KEGG Source Files 72 KEGG source files are available for download from ftp ftp genome ad jp pub kegg This direc tory has a number of subdirectories including expression genomes ligand pathways and tar files Only the Ligand database can be imported into Vector PathBlazer The Ligand database Database of Chemical Compounds and Reactions in Biological Pathways is designed to pro vide the linkage between chemical and biological aspects of life in the light of enzymatic reac tions The Ligand database is a major component of the DBGET LinkDB integrated database system http www genome ad jp dbget providing useful links among databases such as Gen Bank and SwissProt The Ligand database consists of three parts the Compound file the Enzyme file and the Reac tion files Files are located on the KEGG ftp site in the directory ftp ftp genome ad jp pub kegg ligand Download the following files from the ligand directory to a single directory on your local file sys tem The information below applies to KEGG version 26 and later versions e compound e enzyme e reaction e reaction_main st e reaction I st e genome An additional reaction file is required and is located on the same KEGG ftp site in the directory ftp ftp genome ad jp pub kegg ligand release 20 Download the following file from the release 20 directory to
250. p as a template select the Save this map as a template checkbox and name the template in the Template Name field Figure 8 12 Click Next Specify an Import Name l a x Import Name DeRise diauxic shift Import Subset E All Experiments v Save this map as a template hemplate Name lt Back Cancel Help Figure 8 12 Specifying an import name for the currently expression data file 6 The next screen is for associating the expression values defined by the current file with one or more pathways that contain components included in the mapping For example in the previous step the enzyme components of the glycolysis pathway were mapped to gene names and in the following figure the glycolysis pathway that references these compo nents is selected Click Add and select a pathway from the database The pathway is added to the Destination Pathways list box To add other pathways click Add again To remove a pathway association select the pathway in the list box and click Delete Destination Pathways x Destination Pathways Glycolysis Pathway Add Delete lt Back Cancel Help Figure 8 13 Associating expression values with pathways To save the expression values in the data file the component to gene name ID map and the pathway associations to the database click Finish Continue to the next section to assign dis play colors to expression value ranges Creating a Tab Delimited Data File of Expres
251. porting TransPath Data rrua 96 oporne B UNSA 97 DIP Source Piles and Import Loe ar aaa gei 97 Instructions for Importing UAE 99 Hapo nne MARA BE br AAE 100 Instructions for Importing User PPI Data ra aa aa arata 100 Importine Proprietary Data eik araka aaa 102 Dengine Sa RUE 102 IDE TINMIO REIC datea aiete araketa E S 103 Delin nS KM 104 Instructions for Importing Proprietary Data ain aea iS E EE 105 Pres De timed RUA BAA 107 Chapter 5 Drawing BGAE 109 Introduction to Drawing Pathways rra 109 RE a aala 110 Drawno aA New PAtn Way iiss aaa aei olla eae 112 Chapter 6 Automatically Assembling Pathways cccccssecseeeceeeeeeeeneeeseeeeeeeesees 133 MNO GUC ziana MEE 133 Pathway Assembly Parameters aria dik a argk 134 DPCCi yO Params paia atata E N 134 Selecting Components and Reactions nen 134 Using Component Subsets to Limit Pathway Interactions aa 135 Limiting the Number of Steps Between Component a 136 Specifying Pathway Direction and Interaction Generality a 137 Pathway Colors in the Graphics Window rruna 138 Assembling Metabolic Versus Discovery Pathways rss 138 Adding Stepwise Reactions to Pathways rss 138 Building Pathways by Selecting Reactions in the Database Explorer 139 Examples of Automatically Assembling Pathways rrura 139 Before Xou Pye OTN eaascett Sus ashi d enna aad etna Aaaa 139 Building a Pathway from a Starting Component a 139 Building a Pathway from a Starting Component to an Ending Comp
252. r s Manual PubMed http www ncbi nim nih gov entrez PubMed Literature query fcgi cmd Retrieve amp db Pub Med amp list_uids s amp dopt Abstract SCOP http scop mrc Imb cam ac uk Struct Class Of Prot SCOP Link scop search cgi key 2 7 1 1 SwissProt Protein http www expasy org cgi bin SwissProt Protein Link Entry niceprot pl P17709 TransPath http www biobase de cgi bin bio TransPath base transpath 3 4_demo bin get cgi s VNTI DNA RNA vnti DNA RNA s VNTI DNA RNA VNTI Protein VNTI Protein s VNTI Protein VNTI Citation vnti CITATION s VNTI Citation VNTI BLAST vnti BLAST s VNTI BLAST Table 4 7 Pre defined URLs Continued 108 CHAPTER DRAWING PATHWAYS This chapter describes how to draw pathways in the PathBlazer Viewer Many of the tasks in this chapter are described using glycolysis as an example to illustrate various functions in the context of a well known metabolic pathway Topics in this chapter include e Introduction to Drawing Pathways on page 109 e Drawing Tools on page 110 e Drawing a New Pathway on page 112 Introduction to Drawing Pathways A key feature of Vector PathBlazer is the ability to draw known and novel pathways by combin ing public and proprietary data Pathways can be drawn in the Graphics window in the following ways e by creating new components and connecting them into reactions e by adding existing components in the database and connecting them into react
253. r s Manual vill CHAPTER INTRODUCTION TO VECTOR PATHBLAZER Overview Welcome to Vector PathBlazer 2 0 part of a family of software packages developed by Invitrogen Bioinformatics Frederick Maryland Other life science applications developed by Invitrogen include Vector NTI Advance Vector Xpression LabShare for Vector NTP and Vector NT for Mac OS X You may not have purchased licenses for all of the modules of the Vector products If you would like to do so please contact Invitrogen at the website http www informaxinc com for more information Vector PathBlazer is a desktop solution for managing and analyzing diverse biological pathways and protein protein interaction data Public domain data from KEGG BIND DIP TransPath and BioCyc databases as well as PPI and proprietary data can be combined edited and organized based on your research objectives enabling the discovery of novel pathways Vector PathBlazer integrates with other members of the Vector family of products including Vector NTI Advance and Vector Xpression to manage a complete functional genomics workflow Getting Started with Vector NTI PathBlazer e Tolearn about the Vector PathBlazer 2 0 User s Manual structure review Chapter 1 To read a brief overview of the Vector PathBlazer software review Chapter 2 e To activate your license for Vector PathBlazer 2 0 Refer to the Vector PathBlazer 2 0 Installation and Licensing Guide th
254. r during pathway construction 135 Vector PathBlazer 2 0 User s Manual Note Pooling refers to drawing a component that occurs more than once in a pathway one time in the Graphics window with multiple connectors drawn to the reactions in which it is involved When a pathway is assembled the default is to pool components that occur more than once You can select to not pool components in which case each occurrence of a component in an assembled pathway is drawn separately You can also select a subset that contains components you specif ically do not want pooled such as small molecules or enzymes If a particular component is specified to not be pooled and it is required to build a pathway the displayed pathway will be disconnected For example the pathway A gt B gt C can be built if B is pooled from the reactions A gt B and B gt C If B is not pooled then the reactions A gt B and B gt C are displayed as disconnected reactions in the pathway even though they share B as a common component Hiding components is useful when you want certain components to be used in assembling the reaction but you do not want them displayed Exclude components by selecting the Ignore Paths through these Components checkbox and then selecting a component subset from the drop down list Turn off component pooling by selecting the Don t Pool Components in Subset checkbox and then selecting a component subset from the drop down list Hid
255. r each Vec tor NTI Advance application as well as for Vector PathBlazer and Vector Xpression E License Manager Contact Us Personal Applications Applications Vector NTI Dynamic licenze D Alons AEs eae Biodnnotator Demo mode DI ContigE xpress Demo mode D GenomBench Demo mode D Vector spression Etatic license Vector PathBlazer Demo mode Static Dynamic Trial Close Figure A 3 License Manager Applications tab For a new installation or update of a previously unlicensed installation License Manager opens in Demo mode for all applications For Dynamic and Trial licenses if you are not licensing the entire software package using the same type of license on the Applications tab click in the license type text box of the application for which you wish to specify a license Click the down arrow to extend the drop down menu and select the appropriate license type s Click the button appropriate for the license type you want to register Each option is described in the following sections Static License Dialog Box To configure your static license click the Static button at the bottom of the Applications tab Figure A 3 This opens the Static License dialog box Figure A 4 Static License Josh Brown Organization BotCon Phone number 240 846 3398 E mail address Lbrown dotcom com License H Hardware ID 2 261 0 1 ZAK Kep Key is needed only if you do not have
256. r into the default PathBlazer database or into a new separate database you create before data import To create a database see Creating a New Database on page 10 You must also have downloaded the data files described in KEGG Source Files on page 72 to your local file system Use the following steps to import KEGG data into Vector PathBlazer 1 Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 2 Open PathBlazer Import by selecting File gt Import PathBlazer Import opens displaying the various import options Figure 4 7 PathBlazer Import a E x Select import module POTO Import E coCyc data User PPI Import User PFI data DIP Import DIF data Import KEGG v 26 data Trans lronort Tranas Path data Description b data from KEGG database Release 26 Back Cancel Figure 4 7 PathBlazer Import displaying KEGG v 26 settings 3 In the Select Import Module box choose Import KEGG v 26 Data The Description box reflects the type of data chosen for import Click Next 4 Inthe KEGG Settings dialog box select the KEGG data directory where you downloaded the source files you previously created by clicking the Browse button adjacent the Root 19 Vector PathBlazer 2 0 User s Manual Folder field Locate the corresponding root folder in the Browse for Folder dialog box and click OK The complete path to the folder displays in Root Folder field
257. r the Text View The graphical image as it displays in the Graphics window is printed when the Master View or an Alternate View is printed Any elements that are hidden from view are not printed In the Text View any expanded folder and visible element is printed For a preview of how a Text View or Master Alternate View will print select File gt Print Preview To print the current display select File gt Print Saving an Image Only the contents of the Master View or an Alternate View can be saved to an image file Either all of the contents in the view can be saved to an image file or just the selected contents Images can be saved in the following file formats e JPEG e Bitmap e EMF Use the following steps to save a pathway as an image 1 To select specific elements in the Graphics window use the SHFT key or the CTRL key to multiple select elements or use the Select commands in the Edit menu for example Edit gt Select All Components selects only the components in the Graphics window 2 Select File gt Save As Image In the Save As Image dialog box select an image format from the drop down list in the Type field Figure 3 63 Click the Browse button in the File Name field Navigate to the location where the image will be stored name the image and click OK 4 If objects are selected in the Graphics window then the Visible Window Only and the Selected Objects Only checkboxes are available in the Image Content field Oth
258. ration Several different data bases can be integrated in one PathBlazer database This allows you to make cross database queries build pathways using data from different sources find cross talks between metabolic and signal transduction pathways etc To avoid redundancy data from different databases should be merged and in PathBlazer com ponents are merged by default during the database import Nonetheless source databases uti lize different data models different substance classifications etc and it is inevitable that some components which should be merged will not be while others will be merged incorrectly All merge events are recorded in a log file described on page 71 If two components are merged incorrectly during import you can manually re create a missing component and link it to appropriate reactions There is no automatic way to un merge two components 67 Vector PathBlazer 2 0 User s Manual 68 For more information about merging components manually see Merging Components Manually on page 45 During import of any new database into the Vector PathBlazer database the program compares each entry in the source files to entries in the database by its primary name and synonym A new component being imported is merged automatically with an old like component only if the name or synonym for the new and old components are identical If a component has a classifi cation it can only be merged with a component with t
259. re Vector PathBlazer files which means they can be shared or reopened in the program Click Save The complete path to the file displays in the File Name field To save the pathway and its reactions without annotating them or changing any existing annotations click Save The pathway and reactions are saved to the database or specified file Note that the pathway is saved as the default name and the reactions are unnamed To name the reactions and annotate the pathway reactions and components continue to the next step If reactions in a pathway are not named they CANNOT be saved as independent objects in the database Use the remaining steps to name any unnamed reactions You can however save reactions not going through a pathway See Saving Reactions Not Going Through a Pathway on page 50 In the first screen the Save Pathway screen enter information in the Name Database Validity Disease and Description fields Figure 3 39 The Name field is required The Pathway hyperlink is highlighted in the left pane Click Next to move to the next screen in the sequence which is the Organisms screen or click any hypertext link in the left pane to go directly to that screen The Organisms Locations Reference and Cross Links screens work in the same way and each is highlighted in the left pane when it is the displayed screen The Organisms screen is shown in Figure 3 40 to illustrate how to add an annotation using one of these four screens Ea
260. re only searched by primary name and not by synonym Name the object in the Graphics window first by either double click ing and entering a name or selecting Object Properties from the shortcut menu and entering a name in the Name field in the Properties box When the Component wizard opens the search will be performed by primary name and by synonym This section lists errors that may be encountered when importing data When a proprietary XML file does not contain the attributes lt list_of_substances gt and or lt list_of_interactions gt the error in Figure D 1 is generated Load From Stored XML IE x Read from ML file ERROR Cannot load data from GM File D PathBlazer Proprietary Data dataz xml Storage Status Initiating the loading of components Clean up ancel Figure D 1 Error generated when a required section is missing in the XML file Solution Problem Troubleshooting Appendix D To import a proprietary XML file both of the attributes lt list_of_substances gt and lt list_of_interactions gt must be present in the file even if the attribute is empty For example the following file can be imported successfully even though both of the attributes lt list_of_substances gt and lt list_of_interactions gt are empty lt storage ID BIND Storage gt lt list_of_substances gt lt list_of_substances gt lt list_of_interactions gt lt list_of_interactions gt lt storage gt When an XML fil
261. reen for annotating a pathway Enter information in the fields The Name field is required Click Next or click a hyperlink to move to the next screen The method of entering information in the remaining screens Constants Conditions Organisms Locations Cross Links and Pathways is the same as the method described in step 5 on page 47 49 Vector PathBlazer 2 0 User s Manual 8 Continue clicking Next and using the hyperlinks to finish annotating the reactions in the pathway The final screen that displays is the Save Finish screen You can also click on the Complete hyperlink in the left pane to display this screen Figure 3 44 Click Save to save the pathway and reactions to either the database or the specified file ZOO Save Finish E E x A Pathway Organisms Tou have completed updating all pathway elements Locations Click lt Save gt to save the pathway Reference Cross Links FA Reaction GOO mur d Components 3 Properties Constants Conditions Organisms Locations Cross Links d Pathways Complete Save Cancel Help Figure 3 44 Final screen for saving a pathway Saving Reactions Not Going Through a Pathway To save reaction s independent of a pathway select the reaction s and choose File gt Save Selected Reactions The first dialog box that opens is similar to dialog boxes in the preceding section with the exception that only components and properties appropriate to the selected r
262. rma 115 Vector PathBlazer 2 0 User s Manual tion or Delete to delete the row Click OK Click Next and add Organism in the same man ner Component Locations Ss Tissue Subcellular location Add Edit Delete lt Back Cancel Help Type A Tissue Subcellular location D Figure 5 7 Wizard for creating new components describing a component Ss location source tissue and organism 7 Enter any crosslinks to a component Figure 5 8 A crosslink is a link to either the Vector NTI database or to an external database Click Add and enter information in the Type 116 Drawing Pathways Chapter 5 either database or URL Database for example VNTI DNA RNA and Accession ID fields Click OK Click Next Component Crosslinks URL Database Add Edit Delete lt Back Cancel Help Crossline ei Type Jatabase Database Se Accession ID pe Figure 5 8 Wizard for creating new components adding database crosslinks 8 Enter any synonyms that are associated with the component one at a time Figure 5 9 Click Add enter a synonym name in the dialog box and click OK Click Add to add another synonym Click Finish Synonyms B X SUNON Add Edit Delete Back Cancel Help Figure 5 9 Wizard for creating new components adding synonyms 9 The component is named in the Graphics window and is saved to the database with any anno
263. rs to see the parts of the pathway that are not immediately visible In addition to pathways reactions and components can also be selected in Database Explorer and opened in the Graphics window For instructions see Adding Path ways Reactions Experiments and Components to the Graphics Window on page 36 Open a pathway from a pw file by selecting File gt Open or clicking the Open button Liz on the toolbar In the Open dialog box locate the pw file and click Open The pathway opens in the Graphics window You can also launch PathBlazer Viewer and open a pathway at the same time by double clicking on the pw file Paths to recently opened pw files display at the bottom of the File menu Since a pw file only contains information about an individual pathway and its associated reac tions and components any operations such as searching or adding reactions are only per formed on the data in the pw file For more information about a pw file see Saving PathBlazer Components Reactions and Pathways on page 46 Viewing Pathways Graphically 14 Components are represented in the Graphics window as either text labels or text labels inside shapes The display format of a pathway depends on whether it is represented as a discovery pathway or a metabolic pathway e Ina Metabolic pathway the catalyzing agents that is enzymes are represented as labels unconnected to the assembled pathway The properties for enzymes thus dis played cann
264. rted component is given a default dupl 1 dupI 2 etc meaning duplicate 1 duplicate 2 etc or a user specified suffix If there is already a component or reac tion with the same suffix then the same merge check is applied and an attempt to merge is 69 Vector PathBlazer 2 0 User s Manual made If it is not successful an additional numeric suffix is added to the make the component name unique No further checks are made Data can be merged manually after import For more information see Merging Components Manually on page 45 Import Session Monitor The import process proceeds displaying a monitor to allow you to follow its progress Figure 4 4 When import is finished an import log displays with a report of the import Figure 4 6 PathBlazer Import x E Data are being imported into the PathBlazer Database Reading enzyme 1415 EEE Time elapsed 00 08 Press lt Back to change settings lt Cancel gt to stop import d Back Cancel Figure 4 4 PathBlazer import monitor PathBlazer Import x Status Data have been imported successtully Log User PPI data hawe been parsed Total molecules 720 Total reactions 642 Total pathways 0 EES Back Hert s Close Help Figure 4 5 PathBlazer import log file For information about a permanent log file see PathBlazer Log File on page 71 70 Importing Data Chapter 4 PathBlazer Import Buttons The but
265. ry name and not also by synonym In the first screen of the Component wizard Figure 5 12 select the Select component from database radio button and click the Browse button I Use this wizard to either select an existing component from the database or to create a new one GZ Create new component Select component from database Database Component GO 4 Back Cancel Help Figure 5 12 Wizard for selecting and creating new components 119 Vector PathBlazer 2 0 User s Manual 5 A list of subsets displays in the Open dialog box Select the subset to search the component you are looking for and double click on it or click Open Figure 5 13 To search all compo nents in the database select the All Components subset Open Components All Components Small Molecules Demo Components filter H20 CL molecules Mame Cancel Ea Figure 5 13 Dialog box for selecting subset to search for component 6 Inthe next dialog box select the component you are looking for from the components that display To search a different subset click the ZI button and select a different subset Click Open The selected component is entered in the Database Component field in the Compo nent wizard Figure 5 14 Click Next x Use this wizard to either select an existing component from the database or to create a new one Create new component Select component from database Database Comp
266. s This example describes how to assemble a pathway by entering a from component and a to component Starting component is Glucose ending component is pyruvate number of pathway steps is nine Reaction 1 Glucose ATP hexokinase gt glucose 6 phosphate ADP Reaction 2 glucose 6 phosphate glucose phosphate isomerase gt fructose 6 phosphate Reaction 3 fructose 6 phosphate ATP phosphofructokinase gt fructose 1 6 bisphosphate ADP Reaction 4 fructose 1 6 bisphosphate fructose diphosphate aldolase gt glyceraldehyde 3 phosphate 2 Reaction 5 glyceraldehyde 3 phosphate 2 Pi 2 NAD 2 glyceraldehyde phosphate dehydrogenase gt 1 3 bisphosphoglycerate 2 NADH 2 H 2 Reaction 6 1 3 bisphosphoglycerate 2 ADP 2 phosphoglycerate kinase gt 3 phospho glycerate 2 ATP 2 Reaction 7 3 phosphoglycerate 2 phosphoglyceromutase gt 2 phosphoglycerate 2 Reaction 8 2 phosphoglycerate 2 enolase gt phosphoenolpyruvate 2 H20 2 Reaction 9 phosphoenolpyruvate 2 ADP 2 pyruvate kinase gt pyruvate 2 ATP 2 1 Select Tools gt Build a Pathway gt Build Discovery Pathway 2 Inthe Build a Pathway dialog box select the Build Pathway from Component checkbox and enter Glucose as the starting component 3 Select the Build Pathway to Component checkbox and enter Pyruvate as the ending component In the Include Reactions from Subset field select t
267. s by selecting Edit gt e Select All to select all objects in the Graphics window e Select All Components Reactions Connectors to select all components reactions or connectors e Select All Labels to select all labels Labels are described in Adding Labels on page 131 18 Working with Pathways Chapter 3 Selecting all objects of a certain type is especially useful when you want to apply the same graphical properties to them For more information see Customizing Graphical Properties on page 19 Hide components reactions and connectors by selecting one or more elements in the Graphics window and selecting Edit gt Hide Selected or Hide Selected from the shortcut menu A list of submenus displays in the shortcut menu Select Hide Selected to hide only the selected elements which are hidden from the view with a sign marking their place To hide multiple levels of elements without selecting them all select Hide Children Hide Parents or Hide Neighbors and then select the number of levels to hide from One Level N Levels or All Levels Unhide selected elements by double clicking on a sign If multiple levels are hidden select Hide gt Unhide Children Parents Neighbors You can also select Edit gt Unhide All e Hide Children hides the resulting elements of the selected element s at the selected level For example in the reaction on the right side in Figure 3 13 if A is selected and Hide Children gt One Level is sel
268. s and discusses gene ontology import and assignment to PathBlazer objects Chapter 8 describes how to overlay gene expression data on the topology of a pathway Appendix A describes the License Manager used to license Vector PathBlazer Appendix B includes the Document Type Definition DTD for mapping proprietary data to a PathBlazer formatted XML file for import Appendix C contains a list of references to locations and citations where you can obtain more information about key concepts in Vector PathBlazer Appendix D contains a list of troubleshooting tips for problems that you might encounter when using Vector PathBlazer Glossary contains definitions of terms or phrases used in the context of PathBlazer System Requirements Vector PathBlazer is a single user application that can be installed on a PC only Installation instructions are provided in a separate manual called the nstalling and Licensing Guide for Vec tor PathBlazer The system requirements for Vector PathBlazer are e Microsoft Windows 98 SE second edition NT 4 0 Workstation service pack 6a 2000 ME XP Professional Introduction to Vector PathBlazer Chapter 1 140 Mb Hard Disk space additional space is required to load KEGG BioCyc TransPath and DIP 128 Mb RAM Microsoft Installer Version 2 Web browser Internet Explorer 5 x Netscape Navigator 4 x Note If you have Microsoft Internet Explorer you can automatically check your
269. s then click OK If the program can match the entered name to any components in the database by primary name or by synonym the Select a component dialog box displays any potential matches The search is performed as a string search by primary name and synonym and all partial matches display For example if glu is entered with the intention of finding glucose then the list in Figure 5 11 is returned Note that components such as Glucagon and Glucose 1 phosphate are returned in addition to Glucose Select a component ldu D Glucose ldu Phosphopyruvate hydrat a du D Glucose 6 phosphate B d Glucose 6 phosphate igo E d Hexokinase dio Glucagon B d Glucose 1 phosphate b EK Ga have 18 items have bee Description irr Giz Gage le citrate synthase Nuclear e Aconttase mitochondrial Also acts on 3 phospho D Also catalyses the anomeri D Glucose D mannose D Glucose 6 phosphatase Drawing Pathways Chapter 5 Figure 5 11 Multiple matches can be returned when a name is entered as a partial string If the program cannot match the entered name to any components in the database a Path Blazer message informs you that the component was not found You can open the Component wizard directly by selecting the newly drawn component and then selecting Component Properties from the shortcut menu However when the data base is searched objects are only searched by prima
270. s in import 104 defining reactions in import 103 description 102 import 102 import instructions 105 Protein protein interaction definition 15 Protein protein interactions building pathways 137 drawing 109 215 Vector PathBlazer 2 0 Users Manual viewing 14 pw file description 14 opening in PathBlazer Viewer 14 113 saving to database 51 R Reaction annotation fields 39 copying 33 definition 6 deleting 33 direction 14 drawing in Graphics window 122 hiding in Graphics window 19 modifying saved reactions 127 properties 29 renaming 33 reversing direction 35 viewing in Text View 29 Reaction node definition 14 viewing graphical properties 19 Reactions saving 50 Rearranging objects in Graphics window 17 Renaming component display name 113 Resizing images in Graphics window 17 S Saving pw file to database 51 components 114 119 image formats 63 images from Graphics window 63 pathway to pw file 46 pathway to database 46 reactions separate from pathway 50 reactions to pathway 46 Search setting logical conditions 58 Searching adding results to existing subsets 59 adding results to new subsets 60 configuring conditions 55 57 database for GO annotated objects 61 for objects in database 54 for objects in pathway 53 Non Strict Search 56 results display 58 Strict Search 56 Vector Xpression database 176 with multiple conditions 54 with single condition 54 Search Results display 58 216 Selecting objects
271. sage displays that a path way could not be constructed from the parameters You can then modify the parameters and attempt to build the pathway again You can also add a range of steps for consideration For example if the shortest possible path is three steps but there is also a pathway of four steps and one additional step is specified then both three and four step pathways are displayed If two additional steps are specified then all pathways of lengths three four and five steps are dis played Set the maximum number of steps by changing the value in the Max number of steps field For a pathway to be built this value must be greater than or equal to one and less than or equal to 254 Specify additional steps by changing the value in the Extra Steps field These fields are only available if the Build Pathway to Component checkbox is selected in the Path box Automatically Assembling Pathways Chapter 6 Specifying Pathway Direction and Interaction Generality The Pathway Direction box in the lower right of the Build a Pathway dialog is for specifying pathway direction and interaction generality Pathway direction refers to the direction in which connectors are followed during pathway assembly Connector direction does not necessarily refer to the direction a chemical reaction proceeds biologically If direction should be considered in pathway assembly there are three options Forward the pathway backbone is constructed by follow
272. se value is matched to the lt substance ID gt attribute in the component part of the file The lt list_of_actions gt attribute describes each reaction in the file The name of the actual reaction is determined by matching the value of lt reaction ref gt to lt reaction ID gt in the reaction part of the file Finally each con nector in the reaction is defined in the lt conf_arc gt attribute which describes the from compo nent to its appropriate reaction lt pathway ID glycolysis DB Disease Desrc InternallD 1038 gt lt BioNet ID glycolysis gt 104 Importing Data Chapter 4 lt list_of_agents gt lt agent ID AGENT0001 gt lt substance ref Phosphopyruvate hydratase gt lt agent gt lt agent ID AGENT0O002 gt lt substance ref ADP gt lt agent gt lt agent ID AGENT0003 gt lt substance ref D Glucose gt lt agent gt lt list_of_agents gt lt list_of_actions gt lt action ID INTERACTIONO001 Type unknown gt lt reaction ref Gly 1 gt lt action gt lt action ID INTERACTIONO002 Type unknown gt lt reaction ref Gly 2 gt lt action gt lt list_of_actions gt lt cont_arc from AGENT0003 to INTERACTIONOOO5 TransitionProbability 0 gt lt bidirect gt No lt bidirect gt lt type gt ordinary lt type gt lt weight gt 1 lt weight gt lt conf_arc gt lt conf_arc from INTERACTIONO005 to AGENT0025 TransitionProbability 0 gt lt bidirect gt N
273. sequence analysis tools and citations in the Vector NTI data base and other external databases e displays differential gene expression data from microarrays in the context of a pathway e imports and assigns gene ontology terms and or annotations to PathBlazer objects e launches Vector Xpression 3 1 where an expression experiment selected in PathBlazer displays Vector PathBlazer Database Vector PathBlazer is a single user system and is comprised of a database which stores all the data objects and the relationships between them and a client which allows you to import view and manipulate the objects stored in the database The database is located on the same machine where the program is installed in a file with the extension mdb When you install Vector PathBlazer and start it for the first time a default database called PathBlazer_demo_db mdb is loaded with a set of pre loaded data to C VNT Database PathwayDB The pre loaded data consists of a set of example data you can use to learn the program You can add data to the default database and you can also create new databases Any data you import create or mod ify is saved to the database you specify Main Data Types The Vector PathBlazer database stores four key data types Pathways Reactions Compo nents and Experiments Pathways are made up of reactions which are in turn made up of components Components are elements of a reaction and can be either an input output or bo
274. sion Values If you do not have a licensed version of Vector Xpression 3 1 from which you can send expres sion data directly to Vector PathBlazer 2 0 you can import expression data into PathBlazer 174 Working with Gene Expression Data Chapter 8 using a tab delimited text file This text file contains a list of gene IDs or names and their associ ated expression values for each expression run included in a microarray analysis Examples of e xpression values can be absolute values relative values ratio or log P values The gene list and the associated expression values can be created with Vector Xpression which can export a table containing one row for each gene to be linked to one component in the pathway a one to one relationship Columns in this table represent the ratios of data that will be displayed The expression file can contain as many columns of expression values as necessary and expression values can be from different expression experiments or Expression Runs For exam ple if you want to display six time points where each value represents a normalized ratio raw data control for a set of genes you can include a column of data corresponding to each time point in the file The format of the file that can be read by Vector PathBlazer is the following e The first column has the column header Name and each row in the column contains a gene name e Column 2 through Column n contain the expression values corresponding to each
275. sociated with a pathway None is the only option in the drop down list Once a data set has been selected select an expression run from the Expression Runs drop down list Those displayed are associ ated with the selected Expression Data Set Expression Runs are listed according to the title of the column headers in the data file If no headers are present the expression runs are labeled generically as Run 1 Run 2 etc Expression Data Sets DeRisi Diauxic shitt ii d Expression Runs E hours d Figure 8 17 Drop down lists in the Graphics toolbar for displaying expression data The DeRisi data is use as an example dataset If there are pathway components that map to genes in the Experiment color coded rectangles representing the expression values of the genes display on the pathway components Discovery View or the pathway reaction nodes Metabolic View The color s in the square correspond to the expression value range displayed in the Expression Palette The associated Experiment s also display on the Expression Data tab in the Pathway Properties dialog box 1 DeRisi JL Iyer VR Brown PO 1997 Exploring the metabolic and genetic control of gene expression on a genomic scale Science 278 5338 680 6 Working with Gene Expression Data Chapter 8 Default Display Colors for Expression Values To view expression data on pathway components display colors are assigned to expression value ranges These settings are independent of a
276. ss of is a or a part of its parent For example the child GOterm3 may be a subclass is a of its parent GO term1 and a part of its other parent GOterm2 Note that part of means can be a part of not Is always a part of In other words the parent need not always encompass the child For example in the component ontology replication fork is a part of the nucleoplasm however it is only a part of the nucleoplasm at particular times during the cell cycle Gene Ontologies Chapter 7 Alternatively from the Gene Ontology Browser dialog box you can link to websites with stan dard GO viewers Right click on any gene ontology term in the right pane and click on one of the links to external viewers also listed below Figure 7 4 Gene Ontology Hierarchy Browser apoptosis Find GO Term anti apoptosis GU 0006916 anti apoptosis amp 0 000691 6 apoptosis G0 0006975 apoptosis G0 0006975 apoptosis activator activity G0 apoptosis inhibitor actvity 40 0 apoptosis regulator activity G0 commitment to apoptosis 40 0 DONA damage response SE A OF erriel found E da molecular function G00003674 anticoagulant activity IBU 000843 antifreeze activity 40 00161 2 antiowidant activite 00 0016209 apoptosis regulator actrvity 00 00 Open in GO Browser binding I arisen e catalytic ac Mg cell adhesi EP GO chaperone cG AP Chaperone reserere gd regulator activity iGo ed Clos
277. sults Subset button and in the dialog box that opens enter the Name and Description of the new repository subset Click OK Working with Pathways Chapter 3 Create Subset E E x E Components Ei All Components All Small Molecules Demo Components GI filter H20 SI CL molecules tzi union jbh i intersection jbh Ee GI test Subset Hame kinases Subset Description ee Figure 3 32 Create subset dialog box Delete a subset by selecting it in the List or Contents Pane and clicking the Delete button ba on the Explorer toolbar or Delete Subset from the shortcut menu Click Yes in the confir mation dialog box that opens The All Components Reactions Experiments Pathways subsets cannot be deleted In addition to creating subsets of specific components reactions experiments or pathways you can also create subsets of all reactions in a pathway all components in a pathway or all compo nents in a reaction Create a subset of all reactions in a pathway by selecting one or more pathways in the List Pane and then selecting Create Reaction Subset from the shortcut menu In the Create Reac tion Subset dialog box that opens enter a name and description for the reaction subset and click Create All reactions included in the selected pathways are added to the new subset Create a subset of all components in a reaction or in a pathway by selecting one or more reactions or pathways reaction and pathways cannot be d
278. synonym the program finds a match and names the component anyway For example when attempting to create a new component called bAR beta ardrenergic receptor involved in the G protein signaling pathway the program automatically names the object F actin instead because barbed is a synonym of F actin The searching algorithm treats the component name as a string and finds all instances of the matching string partially or completely The program automatically renames the component if there is only one match in the database If there is more than one match a list of matching com ponents is presented from which you can determine whether any of the options are a true match To resolve this right click on the object and select Change Component Display Name In the dialog box that opens select the display name from those listed You can select an option to change the name in the current image or to change it in all pathways 203 Vector PathBlazer 2 0 User s Manual Problem Solution Import Problem 204 A new component is drawn in the Graphics window and to name it Component Properties is selected from the shortcut menu In the Component wizard the Select component from data base radio button is selected and glucose is entered You know D Glucose is already in the database and that one of its synonyms is glucose but Glucose is not returned When an object is named by this method objects in the database a
279. t lt att gt lt edge gt Importing Data Chapter 4 The following table shows the XML tag that is parsed from the reaction part a description of its value and where the value displays in the program Table 4 6 Description Annotation j in Vector PathBlazer lt edge uid gt Primary name Reaction Name lt edge gt Example DIP 17861E Reaction Crosslink Note Reactions including compo nents named UNDEFINED UNKNOWN Homo sapiens or an empty value are skipped PubMed ID Reaction Crosslinks Table 4 6 XML tags that are imported for DIP components A list of pre defined URLs that are automatically setup for DIP reactions and are placed in the CrossLinks annotation field These are listed in Pre Defined URLs on page 107 Instructions for Importing DIP You can import data either into the default PathBlazer database or into a new separate database you create before the data import To create a database see Creating a New Database on page 10 You must also have downloaded the data file described in DIP Source Files and Import Logic on page 97 to your local file system Use the following steps to import DIP data into the Vector PathBlazer database 1 Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 2 From an open PathBlazer window select File gt Import The PathBlazer Import tool opens displaying the various import optio
280. t is the value of the ENTRY field in the Enzyme file Web Pre defined URLs are listed in Pre UM BBD Biocatalysis Biodegrada Defined URLs on page 107 tion Database BRENDA SCOP Structural Classification of Proteins Pathway Reference to KEGG maps Reaction Pathway Table 4 3 Imported attribute fields from the Enzyme file Continued KEGG Reaction Files The Reaction files are a collection of chemical reactions that appear in the pathway diagrams of the KEGG PATHWAY database as well as in the Enzyme file Reactions include non enzymatic reactions and enzymatic reactions whose E C numbers have not been assigned yet There are three kinds of Reaction files reaction reaction lst and reaction main lst All files include chemical equations Reaction I st file The file reaction Ist lists all reactions appearing in the Enzyme file and the KEGG Pathway data base Each line corresponds to a separate reaction and is given a unique ID Each reaction entry starts with the reaction ID followed by a colon followed by the reaction written as a chemical equation The identification numbers in the chemical equation reference values in the Entry field in the Compound file The following is a partial example of the reaction st file as it appears in a text editor R00702 2 C00448 lt gt C00013 C03428 C00080 A reaction object is created in the Vector PathBlazer database for each KEGG reaction using the reaction ID in the re
281. t Name lt node gt Note Components named UNDE FINED UNKNOWN Homo sapiens or an empty value are skipped lt node uid gt Alternate name Component Synonym lt node gt Component Crosslink lt node class gt Molecule type All molecules in Component Class lt node gt the DIP database are proteins lt att name organ Component Organism ism gt lt att name descr gt Description of the components Component Synonyms lt feature name gt Links to other databases Component CrossLinks Table 4 5 XML tags that are imported for DIP components A list of pre defined URLs are automatically setup for DIP components and are placed in the CrossLinks annotation field These are listed in Pre Defined URLs on page 107 A reaction object is created for each reaction listed in the file The following is a partial example of the part of the file that contains reaction information Values of attributes or elements that are directly parsed are in bold Components are linked to a reaction using the values in the from and to fields in the reaction part of the file which correspond to the value in the id field for a component in the component part lt edge uid DIP 17861E id 1 7692 from 4692 to 1603 class inter gt lt feature name DIP 21686X class exp s gt lt src gt PMID 12011112 lt src gt lt val gt Affinity column lt val gt lt feature gt lt att name class gt lt val gt core lt val g
282. t be merged with Mas 1 from BIND which also has the synonym PEP Because however source databases utilize different data models different substance classifications etc it is inevitable that some components which should be merged will not be while others will be merged incor rectly After import be sure and review all merge events in the log file described on page 71 Some common molecules such as H20 ATP and Na are always merged Merge Results Notes As a result of a merge the name and synonyms of a new component are appended to the syn onyms of the old component During the merge process you have the option to retain old attributes or replace them with attributes of the new component When the import process is finished a Summary of merged components displays indicating what was merged and what and how renaming of objects occurred You can copy this summary to the clipboard and or save it in a file This information is also recorded in the log file described on page 71 PathBlazer Import E 4 i EA Status Data have been imported successfully Lag BIND data hawe been parsed Total molecules 3990 Total reactions ei fe See addi Pon import results in the log file E GEEAE Ea Settingstill INF OAR MASIN CAM Docume Figure 4 3 PathBlazer import log displaying the number of merged objects lf components or reactions with the same name do not meet the criteria described and they are not merged the newly impo
283. t component for the link is royal blue four end components are shaded red The links between the two pathways are aqua blue E Automatically generated pathway 6 Discovery unrestricted view Database ZZ x e d TNF 3 TNFR1 3 Fructose 1 6 bisphosphate ate isomerase osphate 4 Master View Figure 6 16 Glycolysis pathway linked to the TNFR signaling pathway Showing Connections to Data from Other Datasources Description In some instances you may want to build a pathway from a specific set of reactions and then continue building the pathway by adding data from other reaction subsets or datasources This example describes how to assemble glycolysis and then add additional reactions that involve hexokinase Input Starting component is Glucose ending component is pyruvate number of pathway steps is ten Output Same as the output in Building a Pathway from a Starting Component to an Ending Component Steps 1 Select Tools gt Build a Pathway gt Build Discovery Pathway 2 Inthe Build a Pathway dialog box select the Build Pathway from Component checkbox and enter Glucose as the starting component 3 Select the Build Pathway to Component checkbox and enter Pyruvate as the ending component In the Include Reactions from Subset field select the Glycolysis reaction subset Set Max number of steps to 10 Set Extra steps to 0 Select Ignore Paths through these Components and select the Small Molecules subset Se
284. ta sources Figure 4 1 One data type can be imported at a time meaning that if KEGG for instance is selected then it is the only data type public or proprietary that can be imported in the current import session Using the scrollbar choose the supported data types from the avail able list in the Import Module field Importing Data Chapter 4 PathBlazer Import d E x Select import module AOC Import EcoCyc data PPI Import UserPFI data DIP Import CIP data Import KEGG v 26 data Trans Imnart TransPath data Description in data from KEGG database Release 26 Back Cancel Figure 4 1 PathBlazer Import Description The Description field identifies the type of data selected for import from the Import Module field For more information about these databases see Appendix B references Root Folder or Source File Dialog Box Each import type utilizes either a root folder or a source file to designate the datasource for import The dialog box varies according to the datatype being imported Refer to each datatype subsection for information about using this dialog box Root Folder The Root Folder is source folder for data files imported using the KEGG BioCyc TransPath and User PPI import tools Source File The Source File is the datasource for data imported using DIP XML and BIND import tools Merge Option Dialog Box One of the most important features of PathBlazer is data integ
285. tation tions base Example Term http Awww godatabase org dev data base archive latest Unique ID in Database Evidence Type Hierarchy of evidence or confidence in the validity of the annotation Organism Source organisms for the annotation Organ isms are listed from top to bottom in the order of most frequently used Component Component Designates the type of Class Class molecule ID in the original database Values Physical Small inorganic mole Protein cule ion Protein Enzyme Small organic mole DNA cule ion RNA Unknown Protein Sub Designates the type of C class protein Structural Protein only Unknown Values Enzyme Regulatory RNA Subclass Designates the type of RNA only RNA Values Unknown mRNA E C Number Enzyme Commission Protein only String Generic Name String Protein only Synonyms Synonym Alternative names of an object String References None Any comment about an object String Table 3 5 Annotation fields and values for pathways components and reactions Continued Vector PathBlazer 2 0 User s Manual Tab Description eet pia EE Field Reaction R Screen Value s Component C Constants Name Constants that can be associated with reac tions Values Ka association Ky dissociation Kp complex formation Keg equilibrium reverse K complex formation forward Km Michaelis Vmax max velocity Value Value of the constant Number
286. tations To change the graphical properties of an object for example font color and size see View and modify an object s graphical properties on page 19 10 If you choose to select a component from a database press the Browse button Uu to locate the component in the existing database 117 Vector PathBlazer 2 0 User s Manual 118 Drawing an Existing Component You may have components already in the database that you either created by import or by draw ing de novo You can access a component from the Graphics window by first drawing a shape to represent it and then searching the database to name the component and provide any annota tions that have already been attributed to it Adding a component this way is useful if for exam ple you have drawn a component and assigned a set of graphical properties to it and then want to overlay the components annotations on the shape Note Adding an existing component with the drawing tools is similar to adding a new component except to name the component you search the database for the component you want to add and then annotate it further Use the following steps to draw a component and then search the database to name it 1 Select a shape in the Palette window and move the cursor to the Graphics window The cur sor changes to the symbol Click anywhere in the Graphics window to insert the shape When the shape is first inserted it is called lt UNNAMED gt by default The c
287. tes and elements in the BIND _interaction xml file that are imported Continued A list of pre defined URLs that are automatically setup for BIND components and reactions is listed in Pre Defined URLs on page 107 Instructions for Importing BIND BIND currently has several division databases each comprising a separate xml file Each file must be imported separately You can import data either into the default PathBlazer database or into a new separate database you create before data import To create a database see Creating a New Database on page 10 You must also have downloaded the data file described in B ND Source Files on page 81 to your local file system Use the following steps to import BIND data into Vector PathBlazer 1 Backup the database into which the data will be imported For instructions see Backing Up the Database on page 11 2 With PathBlazer open select File gt Import The PathBlazer Import tool opens displaying the various import options Figure 4 9 PathBlazer Import Eo E EA Select impart module Import KEGG v 26 data Ho Import TransPath data ANIL Import of data from 8ML file Description K data from BIND database Next gt Cancel Figure 4 9 PathBlazer Import selecting the BIND import option 3 In the Select Import Module screen of the Import Wizard choose Import BIND Data The Description box reflects the type of data chosen for import Click Next I
288. th way and the total number of reactions that will display As expected the shortest path between glucose and fructose 6 phosphate occurs in three reactions Click Yes to continue After the assembled pathway displays save it in the database Select File gt Save As In the Save Pathway dialog box in the Select a Subset field select Metabolic from the drop down menu In the Name text box enter an appropriate name to identify the pathway such as Pathway Glycolysis 2 steps Based on the selected parameters the program assembles a pathway that consists of the first seven reactions in glycolysis and displays it in the Graphics window Figure 6 3 The starting component is indicated by shading it royal blue The title bar indicates that the pathway is auto matically generated and when you save the pathway the name Automatically generated is Automatically Assembling Pathways Chapter 6 entered as the default in the Name field For instructions on saving pathways see Saving Path Blazer Components Reactions and Pathways on page 46 E Automatically generated pathway Discovery unrestricted view Database Fructose 1 6 bis D o o be GO Fructose 6 phasphate D a e o Master View 7 Figure 6 3 First three steps of glycolysis automatically assembled the font of some molecules has been changed to white Building a Pathway from a Starting Component to an Ending Component Description Input Output Step
289. th of the reaction In Vector PathBlazer components can be any kind of molecule such as protein DNA RNA small molecule etc and can also be physical elements such as heat or light For exam ple the substrates products and enzyme in the first step of the metabolic pathway glycolysis are glucose ATP hexokinase glucose 6 phosphate and ADP and can each be represented as individual components Components can either be imported into the database or created de novo and are stored in the database as individual entities Components can have attributes associated with them such as subcellular localization chemical formula type etc and can also have alternate names or synonyms associated with them Components are named by a unique primary name in the database and synonyms can be used as secondary names Syn onyms are especially useful when searching the database and naming components For exam ple hexokinase can have the synonym glucokinase associated with it and when a search is performed for glucokinase hexokinase is returned as the primary object Furthermore if a syn onym is entered when building a pathway any reactions that include components that match by synonym are linked together by the pathway building algorithm Reactions are groups of one or more components that undergo a transformation Transfor mations are biochemical reactions or interactions between components The types of transfor mations that can be represented in Vector
290. thBlazer 2 0 User s Manual mapping Figure 8 6 Click Add and select a pathway from the database Click Finish to save the expression values in the file and the pathway associations to the database Destination Pathways E x Destination Pathways Glycolysis Pathway Add Delete lt Back Cancel Help Figure 8 6 Associating pathways in the database with a data set 8 The new data set appears in the Expression Data Sets drop down list in the Graphics tool bar when the pathway it is mapped to is open It is listed permanently in the All Experiments folder in the Database Explorer Note These same steps can be used to add new expression data to a pathway Editing a Template Once you have established a mapping between a set of pathway components and gene names IDs the template you have created can be used with other expression data files that have corre sponding gene names You can also edit the mapping by adding additional components or deleting components To change the contents of a template add a template or delete a template use the following steps 1 Select Tools gt Manage Expression Data gt Edit Expression Templates The Expression Import Template Manager opens listing any templates currently in the database Figure 8 7 From this dialog box you can add edit duplicate and delete templates Expression Import Template Manager E EA Templates Teast Mapping Add Edit Duplic
291. the Contact Us tab Figure AT This tab summarizes your Vector software licensing agreement Additionally it provides information for upgrading your Vector application license and contacting Invitrogen f License Manager a x Contact Us Personal Applications Use of this software i subject to the terme and conditions of the Infor as End User License Agreement A copy of the agreement can be found by selecting Start gt Programs gt Informas gt License Agreement You may order 4 license Upgrade for one or all of the component programs via fax email or phone Simply send us your PO or credit card number shipping and billing addresses fax and phone numbers to Phone In the U S 800 357 3114 International 240 379 4000 240 379 4098 galestOintormaxinc com Figure A 1 License Manager Contact Us tab Personal Tab The Personal tab Figure A 2 provides text boxes for entering personal information Once entered on this tab when you click your license choice on the Applications tab your entries are automatically entered on the license application ES License Manager Contact Us Personal Applications Hame losh Brown Organization Pete Phone number 240 846 3398 E mail address JLbrown dotcomcom Close Figure A 2 License Manager Personal tab 184 License Manager Appendix A Applications Tab The Applications tab Figure A 3 indicates the type of License currently in effect fo
292. the actions in the dialog box update Continue to the next step 3 Ifthe added component is named in the Graphics window that is the component has either been named based on an existing database component or a new name has been entered in the database the dialog in Figure 5 25 displays with three options Update reaction Cre ate new reaction and Disconnect this reaction from the pathway The option Update reaction is only available if the reaction does not participate in more than one pathway AN You are about to add a component to reaction i ZE g dt K already existing in the Database ZE EEE Cancel Please select action to take f Update reaction Create new reaction Ee I D Disconnect this reaction from pathway rr a Reaction Name glycolysis raz nono ER E Component Name NOTE In order to add component to a reaction you have to name it firak Figure 5 25 Options when adding a named component to a saved pathway 129 Vector PathBlazer 2 0 User s Manual 130 4 The reaction name for example glycolysis _rxn2 displays in the Reaction Name field and the Component name H20 displays in the Component Name field Select the radio but ton that corresponds to the action you want to apply and click OK See Table 5 3 for action descriptions To change the component that is being added click Component and name the component by following the instructions in either Drawing
293. the same directory on your local sys tem reaction main tar Z 1 http Awww genome ad jp kegg 2 ftp ftp qenome ad jp pub kegg ligand ligand doc Importing Data Chapter 4 Extract the files from the reaction main tar Z file to a subdirectory in the directory in which the files were downloaded with a file extraction program such as WinZip Once extracted numerous rea files are created in a subdirectory A fifth file is needed to assign species names to three letter species codes in the Enzyme file Download the following file from the genomes directory to the same directory on your local file system where the other KEGG files were downloaded ftp ftp genome ad jp pub kegg genomes genome An example of the contents of each file is given below with an explanation of how the informa tion in the file is parsed into Vector PathBlazer and how it references the data in the other files to create a list of reactions with the corresponding components in the database KEGG Import Logic When the KEGG files listed previously are loaded into Vector PathBlazer the following steps Occur 1 Each compound listed in the compound file is created in the database as a component 2 Each enzyme listed in the enzyme file is created in the database as a component 3 Each compound that is not an enzyme is linked to a reaction from the reaction st file 4 The directionality of reactions is determined from reaction_main st file 5 The formula and nam
294. tional reaction In the forward reaction Mol A and Mol B are substrates and are connected to the Forward Rxn node Mol C is the product of the forward reaction and is also connected to the Forward Rxn node All connectors point to the right The reverse reaction is exactly opposite of the forward reaction Mol C is now the substrate and is connected to the Reverse Rxn node by a left pointing connector Mol A and Mol B are the prod ucts and are also connected to the Reverse Rxn node by left pointing arrows Mol A Reverse Ran Mol C Mol D Forward Ren Figure 3 9 Bidirectional reaction with substrates and products Inhibition and Activation of A B gt C Figure 3 10 shows how an inhibiting connector displays as a line a sign in a circle An activating connector displays as a line with sign in a circle Activating Mal Mol A wiol Mol B Inhibiting Mal Figure 3 10 Inhibition and activation of a unidirectional reaction Multimer formation Figure 3 11 shows how multimers dimers trimers etc can be formed in three separate reactions from Mol A In Reaction 1 two molecules of Mol A form a dimer called A2 Likewise in Reaction 2 three molecules of Mol A form a trimer called A3 and in Reaction 3 four molecules form a tetramer called A4 In the database A2 A3 and A4 are each individual components The connectors that are associated with each reaction can be annotated with sto ichiometric constants also For
295. tions a Gi glycolysis Show only connecting components Calculate critical points m Connection Length m Pathway Direction Max Number of Steps Extra Steps Direction Interaction Generality I fo E Forward eleiz z OK Cancel Help LEE Figure 6 7 Building a pathway from one pathway to another component 11 Click OK to start assembling the pathway A dialog box displays informing you of the short est pathway and the total number of reactions that will display Click Yes to continue Based on the selected parameters the program assembles a pathway that consists of the steps from the first two steps of glycolysis to pyruvate Figure 6 5 The starting pathway is shaded light blue and the ending component in the starting pathway is shaded royal blue displayed with white font The ending component is shaded red not shown Automatically Assembling Pathways Chapter 6 The title bar indicates that the pathway is automatically generated and when you save the path way the name Automatically generated is entered as the default in the Name field E Automatically generated pathway 3 Discovery unrestricted view Database a ol x ADP er 6 phosphate Glucose 6 phosphate Master View Figure 6 8 Building a pathway from a starting pathway to a component Building a Pathway Through a Component Description Input Output Steps This example describes how to assemble a pathway by enterin
296. tions from Subset field check the checkbox for the Glycolysis reac tion subset Set Max number of steps to 3 select Ignore Paths through these Components and select the Small Molecules subset containing the small molecules ATP ADP and H20 Select Don t Pool Components in Subset and select the Small Molecules subset Set Direction to Forward Set Interaction Generality to Unlimited The Build a Pathway dialog box should look simi lar to that in Figure 6 2 Build a Pathway E E Fath Build Pathway le from Component from Pathway Glucose Browse Build Pathway I to Component I to Pathway E T Build Pathway through Component Component Subsets le Ignore Paths through these Components bi Small Molecules i M Dont Pool Components in Subset bi Small Molecules a I Hide these Components OA Choose Component Subset Include Reactions from Subsets KL Reactions OEM All Reactions ll glycolysis Show only connecting components Calculate critical points Pathway Direction Direction Interaction Generality Forward ki Unlimited ka ee E Cancel Help Connection Length Mae Number of Steps Extra Steps E d Figure 6 2 Building a pathway from a selected component 10 Click OK to start assembling the pathway A progress bar at the bottom of the window 11 shows the status of the assembly A dialog box displays informing you of the shortest pa
297. to pertinent websites 157 searching database for objects with annotations 61 searching for GO terms 156 updating GO categories 159 viewing GO terms 155 Graphical layouts applying 28 description 24 properties 25 types 24 Graphical properties changing 20 customizing 19 viewing an object s 19 Graphics window adding components from Database Explorer 36 adding labels 131 adding pathways from Database Explorer 36 adding reactions from Database Explorer 36 changing object s graphical properties 20 displaying expression values on components 178 drawing existing component 118 121 drawing existing reaction 125 drawing new component 113 drawing new reaction 122 example reactions 15 finding objects in pathway 53 fitting image 18 hiding and unhiding objects 19 modifying graph properties 24 modifying saved reactions 127 navigating 17 opening 112 opening database crosslinks 52 opening pathways 14 panning an image 17 printing images 63 rearranging objects 17 resizing images 17 saving images 63 selecting objects 18 viewing pathways 13 14 zooming 18 Graph properties modifying 24 H Hiding columns in Database Explorer 32 Database Explorer 13 objects in Graphics window 19 Palette window 12 status bar 11 Hierarchical layout applying 25 description 25 properties 26 Highlighting schema creating 21 hiding 21 I Imporing TransPath 93 Importing BIND 80 213 Vector PathBlazer 2 0 Users Manual BioCyc 85 description of d
298. tons in the PathBlazer Import tool allow you to progress forward or go back to previous screens to change settings prior to starting an import session or cancel the import process Table 4 7 Button Action Reverts the import process back by one screen To return to the desired screen continue clicking the Back button until the screen of interest is displayed Mean Advances the import process to the next screen Cancel Terminates the import process and returns to the user to the Path Blazer Viewer Table 4 1 Buttons and their actions in PathBlazer Import PathBlazer Log File A permanent log file separate from the log file that displays after each import Figure 4 3 is stored in the same folder as the database it was created for For example C Documents and Settings lt My Documents gt My PathBlazer Data PathBlazer_demo_db log The log file a simple text format file is designed for an advanced user to track and reverse changes of DB objects such as pathways reactions and components Su PathBlazer_demo_db log Notepad i File Edit Format Help Activity Import Fri Dec 12 16 50 40 2003 Activity Import Fri Dec 12 16 52 56 2003 Activity Import Mon Jan 05 17 34 01 2004 Component ATE renamed into ATP C dupl 1 Component GTP renamed into GTP dupl 1 Component GDP renamed into GDP Cdupl 1 Component ADE renamed into ADP dupl 1 Activity Import Fri Jan 09 09 23
299. ts are merged during import if they have the same name AND 1 For both of them the Component Class is unknown 2 For both of them the Component Class is the same 3 If the Component Class of one of them is unknown and the option Merge components with known classification with similarly named components with unknown classifica tion is selected Figure 4 2 4 For hierarchical classifications rules 2 and 3 are applied recursively Important Note Importing Data Chapter 4 Two merge examples 1 A component with some classifications and annotations exists in the PathBlazer database When you import the next database it may have some unclassified components including the one already classified in the PathBlazer database You can forbid the merge of classified components with unclassified components and hopefully avoid some hard to fix mistakes 2 Components with the same names and classifications DNA gt Chromosome gt Gene and DNA gt Chromosome gt Centromere would not be merged Components with same names and classifications DNA gt Chromosome gt Gene and DNA gt Chromosome gt Unknown would be merged only if the option Merge components with known classification with similarly named components with unknown classification is selected A merge is not executed if a synonym or name which is used for the merge is less than four symbols For example phosphoenolpyruvate that has the synonym PEP KEGG will no
300. ts borders expand to fill the left side or double click on the its title bar to return it to the left side For more information about using the Palette see Drawing Tools on page 110 The Graphics window cannot be converted to an independent window However you can maxi mize the Graphics window by closing the Palette window and the Database Explorer window described below To close the Palette window click the x in the right corner To view the Pal ette window again select View gt Palette For more information about using the Pathway Viewing Area see Working with Pathways in the Graphics Window on page 13 and Chapter 5 Drawing Pathways Database Explorer The Database Explorer window at the bottom of PathBlazer Viewer Figure 3 2 is for browsing and organizing the contents of the database by the four main data types summarized below For detailed descriptions of the PathBlazer data types see Main Data Types on page 6 12 Working with Pathways Chapter 3 Components are elements of a reaction and can be either an input output or both of the reaction They can be any kind of molecule or physical element Reactions are groups of one or more components that undergo biochemical reactions or interactions between components Pathways are one or more reactions they can be either independent of each other or linked together through at least one component Experiments are expression data whose files are imported into PathBlaz
301. ure 3 35 Annotations are listed in screens when saving an object When an object has been saved to the database its properties are viewed by selecting View gt Properties Properties from the shortcut menu in Database Explorer or Component Connec tor Reaction Experiment Pathway Properties in the Graphics window Master View A screen containing tabs for each attribute type lists the attributes by field Figure 3 36 shows the Properties box for a pathway Annotation Tabs Pathway Properties Cross Links GO Annotations Expression Data General Organisms Locations References Name Datasource Validity Glycolysis Pathway I Universally Accepted bd Annotation Fields Disease Glycolysis Pathway discover view according to Lehninger Description Confidence v Figure 3 36 Annotations are listed in tabs when viewing the properties of a saved object In PathBlazer Database Explorer to batch change annotations to contents of subsets of either components or reactions in the Details View of PathBlazer Explorer left pane open the appropriate Component or Reactions folder by clicking the to its left Right click the compo nent or reactions subset and choose Content Properties The dialog box that opens displays attributes that apply to all contents of that subset Figure 3 37 Working with Pathways Chapter 3 On any of the tabs Organism Location or Description review chan
302. ursor remains a wand until you either click another shape or line in the Palette window click on one of the buttons in the Graphics toolbar such as the arrow icon or press ESCAPE To assign a name to the shape click the arrow icon on the toolbar double click on the shape enter a name and press ENTER If the name matches an object in the database by primary name or by synonym the object is automatically named by the primary name If the entered name does not match an object already in the database or a synonym of an object a dialog box opens allowing you to select among several options related to naming the new shape Figure 5 10 Only options appropriate for your new object type are available New Renamed Component Select Option Eo x AN A component with name new enzyme has not been found in the Database Please select one option Look for components with similar names new enzyme in current fle Look for component new enzyme in main Database fe Look for components with similar names new enzyme in the main Database GETE Create new component new enzyme Cancel Figure 5 10 Select the preferred option for naming or renaming a new component The first three radio buttons allow you to search the database for an existing object s More information about those options are provided in the next section To draw an existing com ponet choose Look for Components with Similar Name
303. use the following steps 1 Delete a connector by selecting it in the Graphics window and then clicking the Delete but ton on the Graphics toolbar or pressing the DELETE key Change one or more connector annotations by selecting a connector in the Graphics win dow and selecting Connector Properties from the shortcut menu Click OK to submit the changes 2 The dialog box in Figure 5 27 opens and displays the reaction to which the connector is linked Yector PathBlazer_ E Lu HEE A GE ihe action br giza the e folowing reactions s which h alteady exist in 3 the Database evi Sta Bette GE SEa Please select the action to take for EE reaction de n S EEE e Ze JActiontotake EL GETE Ge Figure 5 27 Dialog box that displays when changing or deleting a connector from a saved reaction 3 Select an option from the drop down list in the Action to take column See Table 5 3 for action descriptions Note If a reaction participates in more than one pathway the option Update reaction is not avail able Click OK The selected action is applied to the reaction To save the change see Saving PathBlazer Components Reactions and Pathways on page 46 To cancel the change and revert to the previous pathway close the pathway with out saving it and then reopen it Adding Labels In the Graphics window the only object for which a name displays is a component The path way s name displays in the title bar but reaction and connector names do not d
304. ute fields for name reaction metabolic compounds metabolic pathways genes encoding the enzyme for several organisms mainly completely sequenced ones genetic diseases and links to other databases including protein sequence motifs and 3D structural deta Some of these attributes are imported into Vector PathBlazer as component attributes In the Vector PathBlazer database a separate object that is a component of which the type is Enzyme is created for each KEGG enzyme listed in this file The following is a partial example of the Enzyme file as it appears in a text editor The values in bold are the values that are imported into Vector PathBlazer Table 4 3 contains a mapping of the fields that are extracted by the importer a field description and where the value of the field appears in Vector PathBlazer for a component object ENTRY EC 1 1 1 1 NAME alcohol dehydrogenase alcohol reductase CLASS Oxidoreductases SYSNAME alcohol NAD oxidoreductase REACTION an alcohol NAD an aldehyde or ketone NADH2 SUBSTRATE alcohol NAD PRODUCT NADH ketone aldehyde COFACTOR Zinc COMMENT A zinc protein Acts on primary or secondary alcohols or hemi acetals the animal but not the yeast enzyme acts also on cyclic secondary alcohols REFERENCE 1 Branden G I Jornvall H Eklund H and Furugren B Alcohol dehydroge nase In Boyer P D Ed The Enzymes 3rd ed vol 11 Academic Press New York 1975 p 103 190 PATHWAY PATH MAP00
305. utput of the reaction Catalyzing agent means any reaction in which the selected reaction participates as the catalyzing agent If hexokinase were the selected component the reaction above would be returned since hexokinase is the catalyzing agent of the reaction 3 In the Select Subset Search field navigate to one or more reaction subsets Select the checkbox next to each subset and click Search Add Reaction E x Specify the role the component will play in the reactions Hit the search button to find the matching reactions in the database JEA Reactions OE All Reactions IIT Demo Reactions LIZ Protein Protein Interaction Reactior 16 Gend Reactions Eg Gle Reactions I Eg Lem Reactions 016 Ras Reactions pea Figure 5 21 Specifying the direction in which reactions should be searched for a selected component 4 Inthe next dialog box all matching reactions that contain the selected component participat ing in the specified direction are listed Figure 5 22 Information about the components dis plays in three columns Reaction Generality and Formula The Reaction column displays the name of the reaction The Generality column lists the Interaction Generality IG value for reactions that are protein protein interactions For reactions that are not protein protein interactions a hyphen displays in this column The Formula column lists the participating components in a reaction and the reacti
306. which it is included If a reaction is included in one or more pathways it cannot be deleted until it is removed from all pathways in which it is included Pathways can be deleted without affecting associated components or reactions Rename an object by double clicking on the name Enter a new name at the cursor Copy an object by selecting it and then clicking the Copy button E in the Explorer toolbar or selecting Copy from the shortcut menu Paste the reference to the object into another subset by clicking the Paste button EZA or selecting Paste from the shortcut menu You can also select objects in the List Pane and drag and drop them into a subset in the Contents Pane Delete an object by selecting it and then clicking the Delete button OX on the Explorer tool bar or selecting Delete from the shortcut menu Click Yes in the confirmation dialog box that opens Organizing Pathway Data Subsets and folders can be used to organize the data contained in the database The Compo nents Reactions Pathways folders and the All Components Reactions Experiments Pathways subsets are system defined containers and cannot be renamed or deleted However any num ber of user defined folders and subsets can be created 33 Vector PathBlazer 2 0 Users Manual 34 Creating Folders Folders are intended to organize subsets and subfolders A folder can only be created in another folder it cannot be created in a subset Create a fo
307. with PathBlazer 166 licenses 183 opening Experiment in from PathBlazer 177 searching database from PathBlazer 176 sending expression data to PathBlazer 177 tools opened from PathBlazer 166 Viewing object s graphical properties 19 pathways in Graphics window 13 14 pathways in text format 28 Z Zoom features in PathBlazer 18 fitting image 18 in 18 Marquee 18 out 18 Zooming Interactive 18 217 Vector PathBlazer 2 0 Users Manual 218
308. xpand it Click the sign to retract it Pathway folder contains subfolders for the reactions and components that are included in the pathway It also contains subfolders for each type of annotation that can be associated with a pathway including Organisms Locations and Cross Links Figure 3 25 For more information about annotations see Annotating Pathways Components Experiments Reactions and Con nectors on page 37 Ee Pathway GEO Reactions H ASNSYNE RAN WATER GLN L ASPARTATE ATP gt GLT ASM PPI AMF E ASNSYNA RXM AMMONIA L ASPARTATE ATF gt ASM PPI AMF Beg Components asparagine synthetase Ik b L glutamate CSH9NG4 L glutamine CSH1ONZO3 H20 H20 suppressor of ompF assembly mutants 1 AMP fC1OHL4NSoyP Pyrophosphate H407P2 L asparagine C4 HaN2O3 ATP C10H16NS013P 3 L 45P4R TATE C4H7 NO4 EEA NO Ham ZIO Organisms BE Known in E coli Ea Locations bene EJ Cross Links F GO Ga eo GO GO GO GO eo Figure 3 25 Pathway folder in the Text View tab Working with Pathways Chapter 3 Reactions folder contains subfolders for each separate reaction in the pathway Figure 3 26 A reaction is represented by the Ee icon Each connector in the reaction is represented with its corresponding component by the Eo icon The Reactions folder also contains subfolders for each type of annotation that can be
309. y defined attributes in the entry after the last entry that was successfully loaded Problem When a proprietary XML file does not define an attribute correctly in the first entry the error in Figure D 3 is generated All entries that are defined correctly before the incorrect entry are imported into the database before the import halts In the following example a partial file is listed with the opening lt synonyms gt attribute crossed out to indicate it is missing which would cause the error shown in Figure D 3 lt storage ID BIND Storage gt lt list_of_substances gt lt substance ID Prostaglandin E2 9 reductase gt lt list_of_origin _accesses gt lt origin_access gt lt database gt KEGG lt database gt lt access gt EC 1 1 1 189 lt access gt lt item_URL gt http www genome ad jp dbget bin www_ bget ec 1 1 1 189 lt item_URL gt lt extra_data gt KEGG Enzyme Link lt extra_data gt lt origin_ access gt lt list_of_ origin accesses gt lt synenyms gt lt name gt Prostaglandin E2 9 reductase lt name gt lt name gt 5Z 13E 15S 9alpha 11alpha 15 Trihydroxyprosta 5 13 dienoate NADP 9 oxidoreductase lt name gt lt name gt EC 1 1 1 189 lt name gt 206 Troubleshooting Appendix D lt synonyms gt Load From Stored XML Ioj x Read from ML file ERROR Cannot load data from ML File D PathBlazer Proprietarn D ata dataz xml Storage Status Initiating the loading of components Clean up
310. y is also not saved automati cally For instructions on how to save pathways and reactions see Saving PathBlazer Com ponents Reactions and Pathways on page 46 Note You can change the type of connector for example change an inhibition to an activation by clicking on the line representing the connector and selecting Object Properties from the short cut menu In the Object Properties box select a different line style from the drop down list in the Style field and close the box The new style is applied to the connector 124 Drawing Pathways Chapter 5 Adding an Existing Reaction from the Database Explorer Any reaction stored in the database can be added to the Graphics window directly from the Database Explorer In the Database Explorer locate a reaction you want to draw in the Graphics window and select Open from the shortcut menu or double click on the reaction The reaction and all components in the reaction display in the Graphics window Maid 5 20 RG ector PathBlazer 2 Reaction gluco_rxn8 red 2 x File Edit View Tools Layout Window Help BO SW ES KA X IA 8 Expression Data Sets None D Expression Runs Ina a ele oles a moede eee Oe Ee ee x Bg DNA RNA E Enzyme Glyceraldehyde 3 phosphate dehydrogenase Protein Reaction gluco_rxn8 Discovery unrestricted view Database Ee 1 3 Bisphophoglycerate Undefined BE H20 Glyceraldehyde 3 phosphate Normal
311. y selecting a component and clicking the Add button on the left side of the screen The component is added to the Compound column in the center table In the Expression Data list box locate the matching gene name ID select it and click the Add button on the right side of the screen Continue mapping components Working with Gene Expression Data Chapter 8 to gene name IDs The following figure shows the glycolysis enzymes mapped to gene names Figure 8 11 To remove a component or gene from the table select it and press the DELETE key Pathway Components Expression Data Component Gene Hexokinase Hexokinase HXK1 Oia Glucose 6 p EOI Phosphoenolpyruyate Fructose 1 6 FBAI Phosphofructokinase Triose phos TEI Glyceraldeh TDH1 Phosphoglycerate kinase Phosphoglycerate mutase Pi Phosphoqly Pyruvate Link Orphan Genes r Relink All Genes Using DB Links Using Names and Synonyms Using DE Links Using Names and Synonyms lt Back Next gt Cancel Help Figure 8 11 Map screen showing glycolysis enzymes mapped to gene names If you have more than one pathway subset containing components you want to map to gene names from the expression data file currently selected click the Browse button uu uat the top of the Pathway Components section to select another subset and continue map ping components to the genes listed in the expression data file e Link Orphan Ge

Vector PathBlazer 2.0 User's Manual

Contents

Download Pdf Manuals

Related Search

Related Contents