Pathways Explorer User Manual - Case Western Reserve University
Contents
1. name OT name type or role substrate or quantity or Add Organism Add Process Molecule Organism Pathway v name name type or role product or quantity or molecule type or default name or Add Organism Add Process Molecule Organism Add Pathway Process Molecule Organism a It needs two Pathway objects as children of Pathways Explorer Be sure to check the appropriate attributes c To assure that the two molecules are the same you must assign a join i Notice there is an symbol in a yellow square next to the Reset button ii You must drag the yellow square onto the word Molecule for both molecules 1 Position the mouse over the square 2 Hold down the left mouse button 3 While holding drag the mouse over the word Molecule 4 Release the left mouse button The word Molecule is highlighted in yellow 5 Repeat for the other molecule ili You may not assign joins to different types of objects and attributes 3 Open the second pathway name drop down box It contains the pathways with a molecule that is a product such that this same molecule is also a substrate in a pathway named Derivatives and degradation of phenylalanine and tyrosine 4 Close the drop down box without choosing a value 5 Click the Run Query button The output shows the molecule the pathway for which the molecule is a substrate and the pathway for which the mo2. Hz 1 Glutathione Metabolism D ipeptidase L cysteinylglycine 1 Glutathione Metabolism Dipeptidase su 1 Glutathione Metabolism D ipeptidase water 1 Glutathione Metabolism gamma dglutamwvlcyclotransferase L g glutamylamino acid 1 Glutathione Metabolism gamma glutamylcyclotransferase L Cslutamylamino acid 1 Glutathione Metabolism gamma dglutamyltranspeptidase gamma GT aa 1 Glutathione Metabolism qamma dalutamyltranspeptidase gamma GT Amino acid 1 Glutathione Metabolism gamma glutamyltranspeptidase qamma GT Glutathione 1 Glutathione Metabolism gamma glutamyltranspeptidase qamma GT GSH 1 Glutathione Metabolism gamma glutamyltranspeptidase gamma GT Fed glutathione 1 Glutathione Metabolism gamma qlutamyltranspeptidase qamma GT Fed glutathione G SH 1 Glutathione Metabalism Glutamate cysteine ligase L cysteine 1 Glutathione Metabolism Glutamate cysteine ligase L glutamate 1 Glutathione Metabolism Glutathione dehydrogenaselascorbatej Dehydro ascorbate 1 Glutathione Metabolism Glutathione dehydrogenasefascorbatej Glutathione 1 hitathiana haatahaliern lhitathinan dakhudenanenaeafseeoarkhatat mou 1 Mg a b C Cw Like li a ue Le r l aie da S Lasd i Imo 4 RE ObubL Each column in the table is one of the attributes checked in the tree Each process in the table is highlighted in the graph of the pathway Graphs are only drawn when there is exactly one pathway in the table output Now you will export the query outp
3. Version 2 0 Date 7 21 2004 Report 23 Pathway Database System 2 0 Pathways Explorer User Manual Center for Computational Genomics Division of Computer Science Department of Genetics EECS Department Case Western Reserve University Case Western Reserve University Cleveland OH 44106 Cleveland OH 44106 1 Overview The Pathways Explorer tool helps you explore the relationships between pathways processes molecules and organisms 1 1 Starting the Pathways Explorer HE Genomes Pathway Browser 1 1 metabolic pathways File View Query WebResources Customize Help Pathways Explorer L Add Pathway Process Molecule Organism Metabolic Pathways Signaling Pathways Explorer Pathway Organism unspecified l Open the Genome Pathways Browser The window above is shown 2 Click the Explorer tab A 2 Tutorial This section will introduce you to the Pathways Explorer and what you can do with it 2 1 Exploring Pathways Processes Molecules and Organisms l Start the Pathways Explorer You see the following empty tree Pathways Explorer L Add Pathway Process Molecule Organism A The Run Query and Export Query buttons perform output queries discussed later B The Reset button brings you back to this empty tree C Pathways Explorer shown in the white area is the root of the query tree D The Add buttons children of the root are used to insert objects into the query tree 1 Under the root may be added a Pathwa
4. ase sewce H a E zl v name I actonase ESI Ei ao eas reversible 2 a location Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism l Metabolic Pathways Signaling Pathways Esplorer Pathway Biosynthesis and degradation of ascorbate Organism unspecified A Pathways Explorer tab click this to begin B Graph output shows graph output when i Run Query is clicked and its results contain a single pathway 1 the processes in the query output are also highlighted ii A graph button K is clicked C Query output ii Each column is an attribute that was checked in the query tree D Pathways Explorer E Run Query button perform an output query and show results at B and C i Graph output is shown only when the results contain exactly one pathway ii The processes in this one pathway that are in the results are highlighted in the graph F Export Query button perform an output query and place results in iV A tab delimited text file v An XML file Reset button start over Drop down box vi Contains all possible values of an attribute in the database vii The list is limited to those values that are consistent with the rest of the drop down box values in the tree vill You may type a value in the textbox ix Ifthe list is too long but you know part of the attribute s value you may type the partial value then open the drop down box and it will contain those value
5. he pathway name drop down box A second drop down box is added SOUrce x Name Cholesterol biosi or or x or Add Process Molecule Organism Add Pathway Process Molecule Organism 7 Open the newly added drop down box and choose Metabolism of ether lipids This indicates that the Pathway object represents all pathways with either of the two names 8 Click the Process button that is a child of the Pathway A Process object is inserted as a child of the Pathway Pince Explorer Pathway name Cholesterol biosy v 9T Metabolism of etk Ol source Or Process x name Ej or revesibie H or location H or Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism A It behaves similarly to the pathway B The Process has a child Add button for inserting a Molecule or Organism as its child 9 Open the name drop down box for the Process A list is shown with all process names in the database that are in a pathway with either of the two pathway names specified above delta 7 Sterol 5 desaturase delta 7 5teral 5 desaturase 3 Maethylglutacanvl coa hydratase Horta dephosphorylatian Add Proces Acyl coa cholesterol acyltransferase LAT Acuiglyceron phosphate reductase a ial Alkylglcerone phosphate synthase Cholesterol oxidase Cucloartenal synthase delta8 24 Lhalestadien 3beta al delta deltat isomerase Desmos
6. lecule is a product 2 4 More Queries using Joins In this example we will see how to find processes that are reversible in one pathway and irreversible in another pathway l Click Reset to begin a new query tree 2 Construct the following tree M or location or d Molecule Organism M __ ae Bor Ad Add Process Molecule Organism Lal x v name location Or Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism a It requires the use of two different colored squares b Set the blue square to by clicking the right mouse button in the square i Further right clicking will cycle through all the operations 3 Open either process name drop down box both contain the same values It contains the processes that are reversible in one pathway and irreversible in another pathway 4 Close the drop down box without choosing a value o Click the Run Query button The output shows the process the pathway for which the process is reversible and the pathway for which the process is irreversible Ouick Referenc EBlGeriomes Pathway Browser 77 0 metabolic ays editor Run Query Export Query Res Pathways Explorer ACE Pathway E 2 resulta Pathway name Biosynthesis and degradation of ascorbate Process name Glucono 3 lactonase v name Biosynthesis a Biosynthesis and degradation of ascorbate Lactan
7. own box for the Organism A list is shown with all the scientific names of organisms in the database that have a process with the specified process name such that this process is in a pathway with either of the two specified pathway names and this process has a molecule with the specified molecule name Organism common name H or scientific mame H or Ad Mus musculus Add Organism 2 2 Query Execution Suppose you want to list the default name and quantity of all the substrate molecules in the reversible processes of the Glutathione Metabolism pathway along with the process and pathway names We shall now perform this query m Click Reset to begin a new query tree 2 Construct the following query tree name type Or role substrate or v quantity 2 or molecule type or default name or Add Organism Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism a Be sure to click the appropriate checkboxes 3 Click the Run Query button The following output table and graph is shown 45 resulta Pathway name Process name Molecule name Molecule quantity Glutathione Metabolism 5 O xopralinasep ATF hydolyzing S oxoproline 1 Glutathione Metabolism 5 O xopralinase ATF hydolyzing Hz 1 Glutathione Metabolism 5 Oxoprolinase ATF hydolyzing su 1 Glutathione Metabolism 5 Oxoprolinase ATF hydolyzing water 1 Glutathione Metabolism D ipeptidase
8. s that match I Checkbox each object e g Pathway Process or Molecule has a checkbox x Clicking it will check or uncheck all its attributes xi When some attributes are checked and others are not the checkbox is gray Checkbox each attribute has a checkbox to indicate whether it should be shown in the query output C X button this deletes the object e g Pathway Process or Molecule and any of its child objects Add buttons click these to insert an object where the Add button is xii For example if an Add Process button is a child of a Pathway object this button will insert a child Process of this Pathway TOQ UA M Pathways Explorer query tree this is the root of the tree which contains all your query constraints or button click this to add additional drop down boxes having additional attribute values means that the parent object pathway process or molecule represents any object with any of these values zZ References 1 S Newman M Ozsoyoglu A Tree Structured Query Interface for Querying Semi Structured Data SSDBM 2004 2 S Newman A Tree Structured Query Interface for Querying Semi Structured Data 2004
9. sm Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism A It behaves similarly to the pathway and process B It has one child Add button for Organism Lx Open the name drop down box for the Molecule A list is shown with all molecule names in the database that are in a process with the specified process name such that this process is in a pathway with either of the two specified pathway names Molecule x name 21 or name Acyl coenzyme A Acyl Ca A kylaculalyceral quanti Alkvlaluceral Ca default nenzyme 4 coenzyme A L a 5H 0 d Pathway Process Molecule Urganism 13 Select phosphate from this list of molecules and click the Organism button that is a child of the Molecule A Molecule object is inserted as a child of the Molecule Export Query Pathways Explorer Pathway e x name Cholesterol biosy or Metabolism of eth or X source a Process Fry X name Aculation dephi T reversible or location or x Molecule name ohosphate ar quantity El or molecule type B or default name m or Organism common name or scientific name m or parent organism group H or Add Organism Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism A It behaves similarly to the pathway process and molecule B It has no child Add buttons 14 Open the scientific name drop d
10. terol reductase Diacylalycerol cholinephosphotransterase Dimethylally pyrophosphatase Dimethylallyl trans transterase Diphosphomevalonate decarboxplase Ethanolaminephosphotransterase F m a b il dil e nl ala F zrmuai ltr amar Suppose this list was too long in fact all drop down boxes are limited to 300 items We want to find an item called Acylation dephosphorylation Close the drop down box Type dephosphorylation in the text box Open the drop down box once again It will contain ony those values containing dephosphorylation Process name dephosphorylatia 7T rever SAcylation dephospherlation lation dephozphorylatian i NER or MOOD D gt Add Molecule Organism Add Process Molecule Organism Add Pathway Process Molecule Organism 10 Click Acylation dephosphorylation This becomes the current value this indicates that the Process object represents all processes with this name such that it is a member of a pathway with either of the two specified pathway names 11 Click the Molecule button that is a child of the Process A Molecule object is inserted as a child of the Process Pathways Explorer Pathway x name Cholesterol biosy Oo Metabolism of etk i 9r source 2 or Process FRE name culation dephi OF reversible Or location or Molecule K name x Or molecule type or default name or Add Organi
11. ut to a tab delimited text file and into Microsoft Excel a oF Click the Export Query button A file dialog appears Type a file name In the Save as type drop down box choose Text files Click Save A tab delimited text file is created containing the query output Open Microsoft Excel From the Data menu choose Import External Data and then Import Data A file dialog appears Locate the file you just exported and click Open The Text Import Wizard appears Click Finish Click OK The query output appears Y ou may also export the query output to an XML file a Perform steps 4a d but in step 4c choose XML files from the drop down box 2 3 Queries Using Joins It is possible to add more than one pathway process or molecules to the query tree When you do this you can then join one object with another and indicate how they relate For example you can specify that two pathway names should be equal or that one molecule quantity should be less than another molecule quantity Possible operations include lt gt lt or gt In this example we will see how to find all pathways with a molecule that is a product such that this same molecule is also a substrate in a pathway named Derivatives and degradation of phenylalanine and tyrosine l Click Reset to begin a new query tree 2 Construct the following query tree Pathways Explorer v Pathway v name Diervatives and c O source Gr x
12. y Process Molecule or Organism 2 Click Pathway A Pathway object is inserted as a child of Pathways Explorer its children are its attributes Pathways Explorer name gl or source H or Add Process Molecule Organism Add Pathway Process Molecule Organism A Each attribute has a drop down box in which a value may be specified B Each attribute has a checkbox that determines which ones will be shown in output queries C The Pathway has child Add buttons for inserting either a Process Molecule or Organism object as children D Next to the Pathway is a graph button for drawing a graph of the pathway E Next to the Pathway is an X button for deleting the pathway object from the tree 3 Open the name drop down box by clicking the down arrow A list is shown with all the pathway names in the database pu Biosynthesis and degradation of ascorbate Biosynthesis and degradation of Biotin Biosynthesis and degradation of catecholamines Biosynthesis and degradation of histidine Biosynthesis and degradation of thyroid hormones Biosynthesis of aromatic amino acids and of quinone cofactors Biosynthesis of glycerophospholipids ae he i eee ee di PP h PO ee ee Pb ee 4 Click Cholestorol biosynthesis This becomes the current value this indicates that the Pathway object represents all pathways with this name gt Gm 5 Click the graph button A graph of this pathway is drawn 6 Click the or button next to t
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