ToxShield Suite User Manual
Contents
1. ccccceecceeeceeeeeeeeeceeeeeeeeeaeeseeeeeesaaeseeeeeeeseaeeseneees 8 2 Working With Projects and Studies 0000e eee eeeeee 9 2 1 Project Falie Suunnan 9 2 1 1 How to Create and Save a Project eccccecceeeeeeeeeeeeeeeeeeeeeeesaeeeeeneeeeteaeeseenees 10 2 1 2 How to Open an Existing Project ccccecceeeceeeeeeeeeeeeaeeeeeeeeeseaeeeeeeeeestnaeeseenes 11 2 1 3 How to Edit Project Details seasainn inann Rna EE ARE 12 2 1 4 How to Delete a Project ececcececescceceeeeeseceeeeseeeneeeesesaeeeeeestsneeeeeesneeaeeeeeeneeaes 13 2 1 5 How to Return to the Project List Page e ee eceeseeeeeeenneeeeeeeeeaeeeeeeeaaeeeeseeaas 13 2 2 St dy FOAtUreS sicctcctccesecce ese cccssess tees Sess edeud cr vadstauaceteecedareseouabececnzvandectenaxstaunestaeee 14 2 2 1 How to Create and Save a Study ccccececceceeceeeeeeeeeeeeaeeeeeeeeesaeeeeeneeestaeeeeenees 15 2 2 2 How to Open an Existing Study ccceeeeceeeeeeeeeceeeeeeeeaeeceeeeeeeeaaeseceeeesteaaeeeenees 16 2 2 3 How to Edit Study Details ccecccceeeeeceeeeeeeeeeeeeeeeeeeeeaeeseceeesaaeeseneeeessaeeseenes 17 2 2 4 How to Delete a Study cccececcecceeeeeeeeeeeceeeeeeeaeeseaeeeeaaaeeseaeeeeeaaeeseceetenaaeeesaes 18 ToxShield Suite User Manual v Contents 2 3 Preparing Your Data for ToxShield Suite Analysis ss eccesseessseeeeenees 19 2 3 1 What You Need to ProvidE ecsnsousicmnn a 19 2 3 2 How to Prepare Study A2. ToxShield Suite User Manual ToxShield Suite version 2 0 Document Version 1 0 July 19 2006 GENE gt LOGIC The information contained in these materials is intended for use by authorized individuals only and is considered confidential and proprietary information of Gene Logic Inc 2005 2006 Gene Logic Inc Intent of Research Study INTENT OF RESEARCH STUDY The results generated for the ToxShield Suite Prediction are based on an innovative program that utilizes new technology The associated analyses are for research use only COPYRIGHT NOTICE This document and the software and materials that compose the ToxShield Suite Prediction s are protected by copyright law 2005 2006 Gene Logic Inc All rights reserved TRADEMARKS ToxExpress and Gene Logic are registered trademarks of Gene Logic Inc Affymetrix and GeneChip are registered trademarks of Affymetrix Inc Other product and company names mentioned herein may be the trademarks of their respective owners ACKNOWLEDGEMENT This product contains or may contain proprietary Gene Logic Inc gene expression data generated using Affymetrix GeneChip technology sample and other gene data as well as gene annotations from external sources Gene Logic Inc would like to acknowledge the following institutions for providing access to gene annotations National Center for Biotechnology Information National Institutes of Health and the National Library o
3. Analyzing the Cross Project Toxicity Report on page 87 Note You cannot share Project lists with other users Once you have created a Project the following information is stored and printed in the ToxShield Suite Prediction report a Project Name Generally the name of or associated with the primary compound Primary Compound Name The name of the compound you want to analyze Customer Name The name of your company as you would like it to appear in the ToxShield Suite Pre diction report Project Notes Relevant details you provide about the primary compound such as details concerning what might already be known from traditional toxicology assessments This section contains the following topics a How to Create and Save a Project a How to Open an Existing Project ToxShield Suite User Manual 9 Project Features a How to Edit Project Details a How to Delete a Project a How to Return to the Project List Page Related Topics Study Features Preparing Your Data for ToxShield Suite Analysis 2 1 1 Note How to Create and Save a Project Any Project you may have created in a previous ToxShield Suite session is listed in the Project List pane If no Project is listed create one or more of them to begin your analysis We recommend that you name each Project by the primary compound of interest the lead drug candi date or something that you can associate easily with that compound v To create a
4. the marker genes If this contract should change between the time you first ran the ToxShield Suite Prediction for a given Study and the time you add or edit notes you may not be able to access certain model systems or files to which you previously had access Warning FIG 2 Warning message j Saving Project Notes will delete the ToxShield Prediction Report for studies under this Project Do you want to Continue 4 To save the Project notes click OK The ToxShield Suite Prediction report will contain your edited Project notes the next time you run the Study Prediction v To edit Project details for Projects that do not contain a Study 1 On the Project List pane click the name of the Project you want to modify and then click Edit Project Details 2 In the Project Details pop up window make any necessary changes to the following project name primary compound name customer name project notes 12 Working With Projects and Studies ay 3 When you are satisfied with your changes click Update Project Related Topics Project Features Study Features How to Create and Save a Project How to Open an Existing Project jenuew 13SN e1INS PIOIYSXOL How to Delete a Project How to Return to the Project List Page 2 1 4 How to Delete a Project You can delete any Project you created and saved in ToxShield Suite However you cannot retrieve a Project once you have deleted it When you delete a
5. 2 0 arrays RAE 230 2 for Liver and Heart model systems A propri etary conversion algorithm converts the probe set data from the RAE 230 2 array to the corresponding probe sets on the RG U34A array For details see the n Vivo Predictive Toxicogenomics Model Refer ence Guide referred to as the Reference Guide See How to Access the In Vivo Predictive Toxicoge nomics Model Reference Guide and Compound List on page 85 Note The predictive toxicogenomic models to which you have access depends on your agreement with Gene Logic For example you may have access to the Liver Model System but not the Heart Model System Related Topics Getting Started With Your Investigation System Requirements How to Log in to ToxShield Suite How to Log Out of ToxShield Suite How to Change Your Password How to Navigate Through ToxShield Suite Other Sources of Information Getting Started With Your Investigation Gene Logic s powerful toxicogenomic tool helps you to evaluate your candidate compound s potential for human toxicity Knowing a compound s potential for toxicity enables you to rank and advance leads with the most promising clinical profiles and to design more informative preclinical studies Before you begin using ToxShield Suite ensure that you have met the system requirements that enable you to take full advantage of the application Then log into ToxShield Suite to begin the process of pre dicting your compound s potenti
6. A System Administration on page 99 describes tasks available to the administrator at your site Welcome to ToxShield Suite ToxShield Suite Version 2 0 combines user interface software with Gene Logic s proprietary in vivo rat liver and heart predictive toxicogenomic models ToxShield Suite analyzes customer supplied gene expression data from treated and vehicle control tissues to assess and predict toxicity and likely induced pathol ogy ies and to find similar known compounds from the ToxExpress Reference Database Gene Logic s unique combination of gene expression data and multiple metrics helps to rank and prioritize compounds for further downstream development ToxShield Suite automatically generates ToxShield Prediction reports that provide an evaluation of a com pound s potential for human toxicity This potential is determined by applying Gene Logic s proprietary gene expression based predictive models to the Affymetrix gene expression data files CEL files that you provide for your study ToxShield Suite supports predictive toxicogenomic models and uses refRMA Reference Robust Multi chip Average normalized expression data for the following analyses Signal intensity ToxShield Suite User Manual 1 Getting Started With Your Investigation 1 2 Changing genes Outlier detection Gene Logic s predictive toxicogenomic models support Affymetrix GeneChip Rat Genome U34A arrays RG U34A and Rat Genome 230
7. How to Prepare Study Annotation Files The format and content of your study annotation file must conform to those listed below in order to upload it to ToxShield Suite See also How to Annotate Your Study on page 38 a File name lt anyName gt txt where lt anyName gt is whatever name you choose and txt is the plain text file format a Format TAB delimited Content and layout The first row of the file must contain the following column headers in the order shown below Subsequent rows contain the data for each column separated by tabs Sample Compound Time TimeUnit Dose DoseUnit If you upload more than one annotation file at a given time ToxShield Suite annotates the Study with the last file only 2 3 2 1 Valid Study Annotation File Column Headers The following headers appear in the study annotation files Sample Sample CEL file s unique file name excluding path information ToxShield Suite uses the last entry only if the lt anyName gt txt file contains more than one instance of a given file name ToxShield Suite renames the last CEL file should you upload identical CEL files from different direc tories This process makes annotating the duplicates more challenging Compound The name of the compound you used when you created your Study Acompound name can be that of the Primary Compound Vehicle or one of the four additional com pounds ToxShield Suite uses the defa
8. List Page 11 Project Features 2 1 3 How to Edit Project Details You can add or edit Project Notes to any Project you created and saved in ToxShield Suite However Tox Shield Suite deletes the current ToxShield Suite Prediction report associated with the Project when you add or edit Notes In this case you must regenerate the ToxShield Suite Prediction report after you have updated your Project You can edit Project Details other than Project Notes only for those Projects that do not yet contain a Study The changes you make to the Project details are recorded when you update the Project Note Changes you make to a Project are permanent there is no undo option once you have updated the Project with your changes v To edit Project Notes for Projects that contain at least one Study 1 On the Project List pane click the name of the Project you want to modify and then click Edit Project Details 2 In the Project Details pop up window make any necessary changes in the Project Notes text box 3 When you are satisfied with your changes click Update Project A warning message advises you that any ToxShield Suite Prediction report previously generated for all Studies included in the Project will be deleted The number of model systems models and generated files available to you for a Study depends on your com pany s contract with Gene Logic For example you may or may not have access to the Heart Model System or
9. Review outlier data and remove outlier samples from the Study m Choose Models Select models and compounds for analysis Prediction Run predictive algorithms Study Predictions Review results and visualizations and download raw data for downstream analysis The basic steps toward completing these phases are Step 1 Before you begin your study assemble the CEL and optionally the study annotation files along with other details relevant to the study design Step 2 Create a ToxShield Suite Project a workspace for analysis of your primary compound Every Project is a collection of one or more studies all designed to determine the toxicity of a primary compound of interest across multiple tissues or study designs Step 3 Create one or more Studies for your Project Each Study is a collection of files associated with a compound and a particular predictive toxicogenomic model Step 4 Select and then upload the CEL files derived from the gene expression data from the particular Affymetrix GeneChip array on which you based your Study Step 5 Annotate the study to provide ToxShield Suite with information about the design of the Study including dose and time points for the treated samples and their corresponding vehicles Step 6 Map the vehicle cohorts to their associated treatment cohorts Step 7 Initiate the data normalization process Step 8 Review outlier analysis results a Review the PCA scatter plot and correlation heat
10. Study on the Study Information pane click the Study link Related Topics Project Features How to Add Edit Study Notes How to Create and Save a Study How to Open an Existing Project How to Delete a Study How to Return to the Project List Page 2 2 4 How to Delete a Study You can delete any Study you created and saved in ToxShield Suite However you cannot retrieve a Study once you have deleted it Should you accidentally delete a Study you must re create it in the appropriate Project and go through each subsequent phase in the workflow v To delete a Study 1 In the Project List pane select the Project that contains the Study you want to delete 2 In the Study Information pane to the right of the Study you want to modify click Del Delete FIG 7 Study Information pane Delete Study TST_STUDY1 Rat Genome 230 2 0 Heart System ked edit Delete Study TST_STUDY2 Rat Genome 230 2 0 Liver6 System omme E edit del TST_STUDY3 Rat Genome U344 Liver System sd edit del Related Topics Project Features Preparing Your Data for ToxShield Suite Analysis How to Create and Save a Study How to Open an Existing Project How to Edit Study Details How to Return to the Project List Page 18 Working With Projects and Studies pay 2 3 Preparing Your Data for ToxShield Suite Analysis ToxShield Suite supports Affymetrix GeneChip arrays RG U34A and RAE 230 2 During the process of creating a Study yo
11. ccccccececeeseeeeeeeeeeseceeeeseneeeees 36 3 2 6 How to View CEL Files 0 00 cceccececcceceeeeeeceeeeeeeaaeeeeeaeeeeaaaeseeeeeeeaaesesueeestaeeesenes 36 3 3 Annotating YOUR St dyo aa aeeoa anaana aaia AAEN 37 3 3 1 How to Annotate Your Study ecccccecceceeeeeeeeceeeceeeeeeeaaeeeeeeeeesaeeeseeeeesseaeeseneees 38 3 3 2 How to Edit Annotations s sess isin nan R ER 39 3 3 3 How to Delete CEL Files and Annotations ccccccscceceeeeeeeeeeeeeeeeeeeeneeeeeaees 40 3 3 4 Annotation Error Messages eeeeeeeeeeeeeeneeeeeeeeeneeeeeeeeaeeeeeesaaeeeeeeseceaeeeeeneneaeees 41 3 4 MAP Ping CONOP S isnt occ ciec sce aa a e aeaa a aa a a aS e aaa Ea sacnidestdettsvedeszeiaies 41 3 4 1 Howto Map Cohorts sisseseade anaa a a aaea eae 42 3 4 2 Cohort Mapping Errors 0 cccecccceceeeeeeeeeeeeeeaeeeeeneeeeeaaeeeeeeeeseaeesseaeeeseeeeeseeeenaas 42 3 5 Normalizing Your Data ccssecceceeeeeeeeeeeeeeeeeeeeneneeeeeeeesneeeeeeeeseeeeeeeeeseeeeeeeneenes 43 vi Contents 3 5 1 How to Normalize Dala ereere eraann i 43 3 5 2 Normalization Error Sisirin iestescandsxesssecanatens secdtechasdeacsejaesneactdsnesenedetens 44 3 6 REVICWING Outliers sissisotaa ce vensenedecete canes sstdeeeeceneeuacteszeeneee 44 3 6 1 How to Rename a Cohort ccccccecccceeeseeeeeeeeeeeeaeeseceeeeeeaaeeseaeeeesaaeeeeaeeeeeeeeeeeaees 45 3 6 2 How to Identify Outliers isisisi arnasia anann aaah aa a tise 46 3 6 3 How to Navigate the All Genes and Cha
12. files that are older than an allotted number of days generally sixty days and displays a message that tells you how many files have been deleted 5 If you receive a message that a given number of your CEL files have been deleted click Proceed Studies you have completed in ToxShield Suite in previous sessions are not affected by the deletion of CEL files However if you want to re run a Study for which files have been deleted you must first upload the sample files See Uploading Sample CEL Files to ToxShield Suite on page 30 Note You cannot run multiple instances of ToxShield Suite concurrently log in to one instance only Related Topics How to Log Out of ToxShield Suite How to Navigate Through ToxShield Suite How to Change Your Password The Workflow tool bar is both a visual representation of the phases of a Study and a tool set that allows you to navigate between them It ensures that you do not overlook any steps in data preparation by guiding you through the processes of 1 2 3 How to Log Out of ToxShield Suite You must log out of ToxShield Suite before you close the browser window if you intend to continue your studies If you close the browser window accidentally during a ToxShield Suite session you must re launch Internet Explorer navigate to https toxshield genelogic com and then log out v To log out of ToxShield Suite from your current ToxShield Suite session On the Menu bar click Log Out v To lo
13. new Project 1 On the Project List pane click Create a New Project The Project Details pop up window appears If the Project Details pop up windows does not appear ensure that your browser is configured to accept pop ups from the Gene Logic server FIG 1 Project Details pop up window PROJECT DETAILS D H PROJECT NAME In the field above type the name of your Project Generally this is same as the primary compound name You can enter upto 25 characters Primary Compound Name In the field above type the name of the compound that you want to analyze Note Although a study can contain more than one compound type the name of the primary compound of interest only Customer Name In the field above type the name of the company organization or person responsible for the Project as you would like it to appear in Tox Shield Suite Prediction report Project Notes In the field above type any additional information about the Project or primary compound under investigation This information will appear in the Tox Shield Suite Prediction report Create Project 10 Working With Projects and Studies pay 2 In the Project Name field type the name of your Project You can enter up to 25 characters Apostro phes are not permitted 3 In the Primary Compound Name field type the name of the compound under investigation You can enter up to 25 characters Apostrophes are not perm
14. Genes Spreadsheet cccceeceeeseceeeeeeees 71 4 2 3 10 Analyzing the Prediction Results by Cohort Spreadsheet ccceeeeeeee 71 4 2 3 11 How to Access the Prediction Results by Cohort Spreadsheet 00cceee 72 4 2 4 Modeling Results Tab Features cccceeeeccseceeeeennneeeeeeenaeeeeeeenaaeeeeeeenaaeeeeeeeaaas 73 4 2 4 1 Model Abbreviations Used in the Model Results Tables ccceeeesseeeeeeenees 74 4 2 4 2 Analyzing the Reference Distribution by Sample Plot ccccceeeseeeeeseeeees 75 4 2 4 3 Analyzing the Prediction Results by Sample Spreadsheet ccceeeeeee 76 4 2 4 4 How to Access the Prediction Results by Sample Spreadsheet e ee 76 4 2 5 Compound Similarity Tab Features cccccceeceeceeeeeeeeceeeeeeeeeeeaeeseeeeeeeeeaeeeeeas 77 4 2 5 1 Analyzing the Most Similar Compounds Table cccceceeeeeseeeeeeeeeeeeneeeees 78 4 2 5 2 Analyzing the Compound Similarity Results Spreadsheet cccceeeeeeee 79 4 2 5 3 How to Access the Compound Similarities Results Spreadsheet 006 79 4 2 5 4 Analyzing the Significance Ranges Table cccccccesseeeeceeeeeeeeeeteeeeeeeeeees 80 4 2 5 5 Analyzing the Ranked Compound Similarity Heatmap sceceeeeeeeeeneeeeees 82 4 2 5 6 Analyzing the Reference Matrix cceccscceeeeeeceeeeeeeeeeeeeeeeeeeeeeeeeeeseneaeeeeeeeeaaaeees 83 4 2 5 7 How to Access the Re
15. Project you delete all associated Studies as well Therefore if you delete a Project you will not be able to retrieve data or results from any of its Studies v To delete a Project 1 In the Project List box click the name of the Project you want to delete and then click Delete Selected Project 2 Do one of the following on the confirmation pop up dialog box that appears To delete the Project click OK If you decide that you do not want to delete the Project click Cancel Related Topics Project Features Study Features How to Create and Save a Project How to Open an Existing Project How to Edit Project Details How to Return to the Project List Page 2 1 5 How to Return to the Project List Page You can return to the Project List page at any point during your ToxShield Suite session v To return to the Project page On the right side of the banner at the top of any page click Projects 13 Study Features 2 2 Warning Related Topics Project Features Study Features How to Create and Save a Project How to Open an Existing Project How to Edit Project Details How to Delete a Project Study Features The Study Information pane displays details pertaining to the Study or Studies within a selected Project A Study is a Project element that represents a collection of Affymetrix CEL files associated with a com pound and a particular organ that spans multiple time points and potentiall
16. Y THIS DOCUMENT Contact Information pay CONTACT INFORMATION For additional details please contact Gene Logic Customer Support at USA and Europe Gene Logic Inc 610 Professional Drive Gaithersburg MD 20879 Phone 1 800 Genelogic or 1 301 987 1700 Japan Gene Logic K K 15F Cerulean Tower 26 1 Sakuragaoka cho Shibuya ku Tokyo 150 8512 Phone 1 81 3 5456 5430 or 1 301 987 1700 Or contact Gene Logic s Global Technical Support at Web htip www genelogic com supporl jenuew J9Sfp INNS PIOIYSXOL This page has been added to accomodate duplex printing CONTENTS 1 Predicting Compound Toxicity With ToxShield Suite 2 0 1 1 1 Welcome to ToxShield Suite cccssecccssccesseeeeeeseesseeeeeseeeeseeeeeeeeeesenseeeensnees 1 1 2 Getting Started With Your Investigation ccsccsssseeessesesseeeeeeseeeneeeeeeeeees 2 1 2 1 System REquireMent ccccecceeececeeeeeeeeeeseaeeeeeneeeceaaeeseaaeeeseaeeeseaaeseeeeeeteaeeeeeaes 3 1 2 2 How to Log in to ToxShield Suite ccceccccececeeeeeeeeeeeceeeeeeeeeeaeeeseeeeeseeeeseeeeee 3 1 2 3 How to Log Out of ToxShield Suite ecccccceeeeeeceeeeeeceeeeeeeeeeeeaeeeeeeeeeeeaeeseeeees 4 1 2 4 How to Change Your PaSSWOMd c cccceeeceeeeeeeeeeeeeeeeaaeeeeeeeeeeaaeeeeeeeeeeaaeeeeeeeess 5 1 2 5 How to Navigate Through ToxShield Suite cccccceeseceeeeeeseceeeeeeeeeseeeeeeneees 6 1 2 6 Other Sources of INfOrmatiOn
17. ain This ensures that you typed the new password exactly as you had intended 5 Click Change Password or to return to your Project without changing your password click Cancel Your password takes effect the next time you log in to ToxShield Suite Related Topics How to Log Out of ToxShield Suite How to Navigate Through ToxShield Suite Getting Started With Your Investigation 1 2 5 How to Navigate Through ToxShield Suite The Project Home page appears once you have logged in to ToxShield Suite It displays the following aids to navigation FIG 2 The ToxShield Suite banner Reference Guide Projects Home cene Loaic F Banner INFO Welcome lanthone Date Fri Jan 14 11 48 53 2005 Menu bar on User name Administrati Preferences Current date time Log Out Online Help amp ToxShield Suite The banner at the top of the page displays the following links a Projects Home page Reference Information provides links that enable you to download the In Vivo Predictive Toxicoge nomics Model Reference Guide Reference Guide and the Compounds Used to Build Models spread sheet The Menu bar displays the following a User name Current date and time a Link to the Administration pages displayed only if you are an Administrator a Link to Log Out Link to Preferences a Link to the online Help Once you have created a Project and have created and opened a Study the Workflow tool
18. al for toxicity This section contains the following topics a System Requirements How to Log in to ToxShield Suite How to Log Out of ToxShield Suite a How to Change Your Password How to Navigate Through ToxShield Suite Other Sources of Information Related Topics Welcome to ToxShield Suite Project Features Predicting Compound Toxicity With ToxShield Suite 2 0 tie Study Features Preparing Your Data for ToxShield Suite Analysis 1 2 1 System Requirements ToxShield Suite is a Web based application requiring Microsoft Internet Explorer 6 0 or higher Data transmission occurs via a 128 bit encrypted secure socket layer SSL connection This typically requires ports 80 and 443 to be open in a firewall jenuew 13SN e1INS PIOIYSXOL Gene Logic has not tested and does not fully support ToxShield Suite running on Apple Mac OS X Gene Logic recommends that you use the Safari Web browser the default browser for Mac OS X In addition to the browser requirements please ensure that you install the following before your first Tox Shield Suite session a J2SE Java Runtime Environment JRE 1 4 2_05 or later available for download at http java sun com j2se 1 4 2 download html by clicking Download J2SE JRE a Adobe SVG Scalable Vector Graphics 3 01 or later viewer available for download at http www adobe com svg viewer install main html Adobe Reader available for download at
19. bar displays icons that represent each phase of the analysis FIG 3 The ToxShield Suite Workflow tool bar Workflow tool bar Completed phases Analysis phases Current phase Next phase Incomplete phases You can return to any completed phase by clicking the appropriate phase icon Note The way in which you navigate between Study phases may affect the workflow For details see Navigating Between Analysis Phases on page 23 Predicting Compound Toxicity With ToxShield Suite 2 0 og Square icons in the Workflow tool bar represent phases in which you enter information about your Study circular icons represent analysis phases during which no action is required on your part The carat symbols gt between icons on the Workflow tool bar indicate the order in which you proceed through the various phases of the investigation The symbol below an icon indicates your current phase As you progress from phase to phase the icons change from light to dark colors ToxShield Suite s interactive web interface guides you through your compound study workflow in a series of phases as follows FIG 4 The ToxShield Suite workflow gt 2 2 R DARK Samples Samples Q Outliers Models Ci p Load Samples Upload CEL files to Gene Logic servers via the web jenuew 13SN e1INS PIOIYSXOL Annotate Samples Upload your study design Data Normalization Perform RMA normalization and outlier analysis Review Outliers
20. eeeeeeeseceeeeeneeeeees 60 4 1 2 Errors That Can Occur During Prediction 0 ccccecccceeeeneceeeeeeeeeeeeeeeeeeeeeeees 60 4 2 Interpreting Prediction Results cceceseeceseeeeeeeeeeeeneeeseeeesneeseseesnenseeeeeenes 60 4 2 1 How to Display Prediction Results cceeeecceceeeenceeeeeeeenaeeeeeeenaeeeeeeeaaeeeeeenaas 61 4 2 2 How to Delete a Prediction cccceeccceceeeeeececeeeeeeececeeseseeceeeesteneeeeeeeneeeeeeeesneeaes 62 4 2 3 Overview Tab Features 0 cceecccecceseceeeeeeeeeaeeeeeneeesaeeeeeeneeseeaeeeeeeeeeeeaeeeeenaeeeeaas 63 4 2 3 1 Analyzing the General Modeling Summary ccccceeeteeeeeeeeeeeeeeeseeeeeeeeeetees 63 4 2 3 2 Analyzing the Overview Table of Most Similar Compounds ceeeeeeeees 64 4 2 3 3 Analyzing the Compound Similarities Spreadsheet ccccceeeeeeseeeeeseeeeees 65 4 2 3 4 How to Access the Compound Similarities Spreadsheet cccceeeeeeeeeees 65 jenuew Jasp INNS PlalySxoL vii Contents 4 2 3 5 Analyzing the Modeling Results Table cccccceeesseeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaeees 66 4 2 3 6 Analyzing the Reference Distribution by Cohort Plot cccccsseeeeeeeesneeeees 67 4 2 3 7 How to Access the Results Distribution Plot eee eeneeeeeeeeneeeeeeeenaeeeeeeeeaas 69 4 2 3 8 Analyzing the Contributing Genes Spreadsheet cscccceeceeeeeseeeeeeeeeeeeeeeees 69 4 2 3 9 How to Access the Contributing
21. ess and hold the Alt key while you press the Tab key until the Internet Explorer or other browser icon is selected Then release the Alt key jenuew 13SN e1INS PIOIYSXOL Related Topics Project Features Preparing Your Data for ToxShield Suite Analysis How to Create and Save a Study How to Edit Project Details How to Delete a Study How to Return to the Project List Page 2 2 3 How to Edit Study Details You can modify the details of any existing Study or change the Study name without any loss of data asso ciated with that Study at any point in the Workflow prior to data normalization v To edit Study information 1 In the Project List pane on the Projects page select the Project that contains the Study you want to change 2 In the Study Information pane to the right of the Study you want to modify click Edit Note You cannot edit a completed Study FIG 6 Study Information pane Edit Study TST_STUDY1 Rat Genome 230 2 0 Heart System Edit Study TST_STUDY2 Rat Genome 230 2 0 Liver6 System Bl edit del TST_STUDY3 Rat Genome U344 Liver System edit del Note You cannot change the Model System with which you have associated the Study To change the Model System delete the current Study and then re create it using the appropriate model 3 In the Study Details pop up window modify the Study details and then click Update Study 17 Study Features 4 If you want to return to or begin working on a
22. f Medicine HomoloGene RefSeq GenBank Unigene and LocusLink Gene Ontology Consortium Gene Ontology GO ENZYME EC Nomenclature International Union of Biochemistry and Molecular Biology Institute for Chemical Research Kyoto University Kyoto Encyclopedia of Genes and Genomes KEGG Minoru Kanehisa PROPRIETARY AND PATENT PENDING INFORMATION This product contains proprietary Gene Logic Inc gene expression data Toxicity Markers predictive algorithms and improvements to well established gene classification methods that are considered confidential property of Gene Logic Inc ToxShield Suite and markers are awaiting patent approval in several Patent Offices throughout the world Further all Gene Logic gene expression data was generated using Affymetrix GeneChip technology Individual sample and gene annotations from external sources have been supplied to assist in interpretation of the results WARRANTY THIS DOCUMENT IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EXPRESS OR IMPLIED WITH RESPECT TO THE CONTENTS OF THIS DOCUMENT INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES FOR THE DOCUMENT S CORRECTNESS ACCURACY RELIABILITY CURRENTNESS MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE NEITHER GENE LOGIC OR ITS AFFILIATES SHALL BE LIABLE TO RECIPIENT OF THIS DOCUMENT OR ANY OTHER PERSON OR ENTITY WITH RESPECT TO ANY LIABILITY LOSS OR DAMAGE CAUSED OR ALLEGED TO HAVE BEEN CAUSED DIRECTLY OR INDIRECTLY B
23. ference Matrix eeeeccceeeeeesneeeeeeeenaeeeeeeenaeeeeeeeeaaeeeeeseaaas 85 4 2 6 How to Access the In Vivo Predictive Toxicogenomics Model Reference Guide and Compound LiSt acctces sevecdners ai eeteessiaceventsse recta aa aa aa AE eased 85 4 2 7 How to Print Information Provided in the Tab Views eessen 86 4 3 Analyzing the Cross Project Toxicity ReEPort csssecssseseseeeeeseeseneeeeeeees 87 4 3 1 How to Generate a Cross Project Toxicity REpOrt ccccccesseeeeereeeesteeeeeees 88 4 3 2 How to Access and Navigate the Cross Project Toxicity Report 89 4 4 Analyzing Data Visualizations in ToxShield Suite csssecesseeeseeeeees 91 4 4 1 Data Visualizations in ToxShield Suite c cccccceeceeeeeeeeeeeeeeeeeeseeeeseneeeeeaeeees 91 4 4 2 Data Visualizations in the ToxShield Suite Prediction Report cseeeeeee 92 4 4 3 Analyzing the Model Distribution Plot 0 eeceeeceeeeeeeeeeeeeeeeeeeeeeeeeneeeeeeeeeeeeaeeees 94 Working With ToxShield Suite Predictions 0555 95 5 1 ToxShield Suite Prediction Features s ccccssccssseceseecesseeeeneeteessseeseneeeeens 95 viii Contents if 42 5 1 1 How to Access and Save the ToxShield Suite Prediction Report and Supporting Fil Sirssrcseiiraniean ae RA 96 S a o J E o Appendix A System Administration 200e eee eee 99 5 E A 1 Creating USer ACCOUNIS i ccniecediced secceecsscctessaceceshiecese
24. g out of ToxShield Suite if you have closed the browser window 1 Open the Internet Explorer browser and then navigate to the ToxShield Suite site at https tox shield genelogic com 2 In the Log In box type your user name and password in the fields provided and then click Log In Because you did not log out of your session prior to closing the browser window the system thinks that you are still logged in to ToxShield Suite and will not allow you to log back in until you have logged out first Predicting Compound Toxicity With ToxShield Suite 2 0 i i FIG 1 Log In box Eoleg i lanthone Already logged in Log out of your current session LogIn Log out jenuew 49Sf UNS PIOIYSXOL 3 At the bottom of the Log In box click Log out You now can log back in to your ToxShield Suite session Related Topics How to Log in to ToxShield Suite How to Change Your Password How to Navigate Through ToxShield Suite Navigating Between Analysis Phases 1 2 4 How to Change Your Password You can change your password as needed after you have logged in to ToxShield Suite v To change your password 1 On the ToxShield Suite banner click Preferences 2 In the Current Password field type the password you used to log in to the current session 3 In the New Password field type your new password A password can contain from 6 to 15 characters 4 In the Confirm Password field type the new password ag
25. hitp www adobe com products acrobat Related Topics What You Need to Provide How to Log in to ToxShield Suite Valid File Types and Formats 1 2 2 How to Log in to ToxShield Suite To log in to ToxShield Suite you must have a user name and password In general your ToxShield Suite Administrator creates these for you Note Itis important that you log out of ToxShield Suite before you close the browser window If you close the browser accidentally you must open a new browser and then log out of and back in to ToxShield Suite See How to Log Out of ToxShield Suite on page 4 v To log in to ToxShield Suite 1 Open the Internet Explorer browser and then navigate to the ToxShield Suite site at https tox shield genelogic com 2 If you are logging in to ToxShield Suite for the first time read and accept the license agreement 3 In the User Name field on the ToxShield Suite Login page type your user name 4 In the Password field type your password and then click Log In Note Ifyou are logging in after having accidently closed the browser during a ToxShield Suite session follow the instruc tions provided in How to Log Out of ToxShield Suite on page 4 Getting Started With Your Investigation ToxShield Suite stores the CEL files you upload for your Studies for sixty 60 days although this time frame may be different for your system The system checks the age of your CEL files each time you log in deletes CEL
26. itted 4 In the Customer Name field type the name of the company as you would like it to appear in the resulting ToxShield Suite Prediction report You can enter up to 25 characters 5 In the Project Notes field type any project related information that you would like stored with the Project The information you enter here is included in the ToxShield Suite Prediction report You can enter up to 10 000 characters jenuew 13SN e1INS PIOIYSXOL 6 Click Create Project located on the lower right corner of the pop up window This step saves your Project and lists it in the Project List box Related Topics Project Features Study Features Preparing Your Data for ToxShield Suite Analysis How to Open an Existing Project How to Edit Project Details How to Delete a Project How to Return to the Project List Page 2 1 2 How to Open an Existing Project The Project List box displays Projects that you have created in previous ToxShield Suite sessions You can open a Project to begin analysis or if necessary make changes to it first v To open an existing Project On the Project List pane click the name of the Project you want to open The Study Information pane is populated with the details of the study or studies associated with the Project you selected Related Topics Project Features Study Features How to Create and Save a Project How to Edit Project Details How to Delete a Project How to Return to the Project
27. ject Details How to Delete a Study Study Assistant Features How to Return to the Project List Page 2 2 2 How to Open an Existing Study When you open an existing Study ToxShield Suite displays the Study Assistant and the Workflow tool bar icons that guide you through the prediction process See also How to Navigate Through ToxShield Suite on page 6 To open a Study 1 In the Project List pane select the Project from which you want to open a Study 2 In the Study list click the desired Study link FIG 5 Study list Study links Study TST_STUDY1 Rat Genome 230 2 0 Heart System BR BB B 2 edit del TST_STUDY2 Rat Genome 230 2 0 Liver System BECRBEBCORB El edit del TST_STUDY3 Rat Genome U344 Liver System Be BB edit del Study links 16 Working With Projects and Studies pay The Study Assistant is displayed in the first phase of the workflow that you have not completed Note If your browser appears to be frozen after you open a new Study it is likely that a Security Warning pop up dialog box is hidden behind the ToxShield Suite window This may occur if you log in to ToxShield Suite and then leave it idle before returning to the browser 3 To access a hidden Security Warning pop up dialog box press and hold the Alt key while you press the Tab key until the Java tea cup icon is selected Then release the Alt key 4 On the Security Warning pop up dialog box click Yes Then pr
28. map images generated using all genes and chang ing genes as determined by a significant fold change b Accept the outliers that ToxShield Suite identified or override the default and indicate any outliers based on your own analysis of the PCA Principal Component Analysis scatter plot or correlation heatmaps Step 9 Select the models on which you want to run the predictive analyses Step 10 Select the compounds against which you want to run compound similarity analyses Getting Started With Your Investigation Step 11 Run the predictive analysis Step 12 Generate ToxShield Suite Prediction the report that summarizes the prediction results Related Topics Project Features Study Features Preparing Your Data for ToxShield Suite Analysis Navigating Between Analysis Phases 1 2 6 Other Sources of Information The comprehensive n Vivo Predictive Toxicogenomics Model Reference Guide referred to as the Refer ence Guide provided with ToxShield Suite provides you with detailed information about the ToxShield Suite predictive toxicogenomics model building process validation methods and compound similarity metrics among others It also contains a full description of the refRMA Reference Robust Multi chip Aver age normalization method You can access the Reference Guide by clicking the Reference Information link on the ToxShield Suite banner Should you need more information contact ToxShield Suite customer suppor
29. ncteessceestatecdsssecesescceesusuesisie 99 S A 1 1 How to Create a User Account s sssssssseessserssseenretiettietsrnsssrnssrnnntnnnnnnnsnnn nnt 99 A 2 Managing Group ACCOUNMS cs ccceescesseeeeeseeeesneseneeeeeseeeseeseeeesseeseeneeeeeeens 101 A 2 1 How to Modify User Accounts Within a GrOup ccceeeeeeeeeesteeeeeeeeeeeneeeees 101 This page has been added to accomodate duplex printing 1 1 PREDICTING COMPOUND TOXICITY WITH TOXSHIELD SuITE 2 0 This user manual is designed to help you understand ToxShield Suite s powerful tools and functions in order to perform your own toxicity investigations It contains the following topics Section 1 Predicting Compound Toxicity With ToxShield Suite 2 0 outlines the contents of this man ual and describes how to get started with ToxShield Suite a Section 2 Working With Projects and Studies on page 9 introduces the concepts of Projects and Studies and explains how you create them from your lab data a Section 3 Conducting Studies on page 23 describes how you design and perform toxicity analyses within a Study a Section 4 Interpreting Prediction Results on page 59 explains the predictive calculation results and data visualizations provided by ToxShield Suite a Section 5 Working With ToxShield Suite Predictions on page 95 provides instructions for accessing the ToxShield Suite Prediction report and the files that support it a Appendix
30. nging Genes Tabs 47 3 6 4 How to Exclude Outliers From Your Study AnalySis ccccseeeeeeeeeseeeeeeees 48 3 6 5 Outlier Erots sciasctevecdedevastecunetacecciustlaacacuueelaantlaancesteceudblaavetdaettianevianchadeviadeesiacdtde 50 3 7 Choosing Predictive Toxicogenomic Models and Compound 50 3 7 1 How to Select Predictive Toxicogenomic Models and Compound6 52 3 7 2 Predictive Toxicogenomics Model Errors ccecceceeeeeeeeeeeeeeeeeenaeeeeeeenaeeeeeeeaas 52 3 7 3 How to Run the Prediction Calculation cccccccccceeeeeeeeeeeeeeeeeeeeeeeeeeaeeseeeees 53 3 7 4 How to Generate the ToxShield Suite Prediction cccccccseeeeeeeeeeesteeeeeees 53 3 7 5 Toxicity Prediction Errors ccccecesceeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeseaeeeeeeseeeeeeeeeeneaeanes 54 3 8 Analyzing the Expression Data and Study Prediction Files 00 55 3 8 1 How to Access the Expression Data Files ecseceeesesneeeeeeenneeeeeeenaeeeeeeeaas 55 3 8 2 How to Access the Study Prediction Files cc ccccceeeeeeeeeeeeeeeeeeeeeessaeeeseneees 57 3 8 3 How to Import TEXT txt Files Into Microsoft Excel eseeeseeseeceeeeeeeeeees 58 Interpreting Prediction ResultS 0000s eee e eee eee 59 4 1 How Gene Logic Determines Toxicity ccscccssseeeeseteeesseeeeeseeeeneeeeeeeees 59 4 1 1 Gene Logic s Threshold Calculation Method ccccececceeseee
31. nnotation FileS cccccccceecseeeeeeneeeeeeeeeeeeeeessaeeeseeeees 20 2 3 2 1 Valid Study Annotation File Column Heade s ccceceeeeeeeeeeeeeeeceeeeseneetees 20 2 3 3 Valid File Types and Format ccccccccececeeeeeceeeeeeeeeaeeeeeeeeaeeeeeeeiaeeeeeeeaeeeeeee 21 Conducting SUGGS i i essa ii iia i a aaa i aa a e aa a ia da Eia a aoa 23 3 1 Navigating Between Analysis Phases ccsssseescseseeeeeeeeeeeneeseesesneeseeesenee 23 3 1 1 Study Assistant Features cccccccceeeceseceeeceeeeeeeeeeeesaeeeeeeeeeceaeeeeeaeeesecaeeeseaeeenaas 26 3 1 2 How to Select a Different Study From Your Project cccccsscsessesesseseeeeeesees 26 3 1 3 Howto Rename a SIUOy ss eicssiencaiiinsd Ghanaian E 27 3 1 4 How to Access Expression and Prediction Result Files ccccsesesesereenees 28 3 1 5 How to Add Edit Study Note sss cosy ueniens aaen aaaeaii 29 3 2 Uploading Sample CEL Files to ToxShield Suite c cceeessseeeeeeseees 30 3 2 1 How to Select CEL File Snsd ana a ae 31 3 2 2 How to Remove Selected CEL Fil S ccccccceeeeeeeeseeeeeeeeeeeeeeaeeeeeeeeeseaeeneeeees 32 3 2 3 How to Upload Selected CEL Files cccccccecesceeeeeeeeeeceeeeeeeeeeeaeeseeeeeesneeneeees 32 3 2 4 CEL File Verification and Error M SSaQe S ccceeceeeeseeeceeeeeeeeaeeeeeeeeeeeaeeenaas 34 3 2 4 1 dava PIUQ In EmO sorsra anina an EAA AESA 35 3 2 5 Selected Uploaded Samples Pane Features
32. sly had access This section contains the following topics a How to Create and Save a Study a How to Open an Existing Study a How to Edit Study Details How to Delete a Study Related Topics Project Features Preparing Your Data for ToxShield Suite Analysis Study Assistant Features 14 Working With Projects and Studies pay How to Select a Different Study From Your Project 2 2 1 How to Create and Save a Study Every Project you create in ToxShield Suite must contain one or more Studies v To create a Study jenuew 13SN e1INS PIOIYSXOL 1 In the Project List pane select the Project to which you want to add a Study 2 In the Study Information pane click Create a New Study The Study Details pop up window appears FIG 3 Study Details pop up window Her To add new Study to a Project type select the required Study information in the fields provided below on the left side Optionally type the name s of any secondary compound s on the right side Rat Genome U344 Liver System ver 6 0 0 Y 3 In the Study Name field type the name for this study You can enter up to 25 characters including percent en dash and period Apostrophes are not permitted 4 In the Vehicle Used field type the name of the vehicle excipient that you used in this Study Although the maximum character length for the vehicle name is 25 we recommend that you limit the name to 13 characters This enables yo
33. t at toxshieldsupport genelogic com Related Topics Interpreting Prediction Results Analyzing Data Visualizations in ToxShield Suite ToxShield Suite Prediction Features 2 1 WORKING WITH PROJECTS AND STUDIES This section introduces you to high level concepts and the background information that helps you to understand how to use ToxShield Suite to predict compound toxicity This section contains the following topics a Project Features on page 9 a Study Features on page 14 a Preparing Your Data for ToxShield Suite Analysis on page 19 Project Features A ToxShield Suite Project is similar to a file folder that contains one or more Studies designed to determine the potential for toxicity of a primary compound of interest across multiple study designs Projects provide the structure for you to perform one or more of these studies each of which represents a predictive toxi cogenomic model system The Project List box in the Project List pane is empty until you have created at least one Project There after ToxShield Suite automatically populates the list box with the name of each Project you create The Project List box also provides a means for you to edit or delete a Project if necessary The Project List pane provides you with access to the Cross Project Toxicity Report which ranks com pound cohorts across your Projects by toxicity scores within each predictive toxicogenomic model For details see
34. u to view and select the treatment vehicle compound names in their entirety during the annotation phase Characters may include percent en dash and period Apostrophes are not permitted 5 In the Model System drop down list select an appropriate model Rat Genome U34A Liver System ver 6 0 0 Rat Genome U34A Heart System ver 3 0 0 Rat Genome 230 2 0 Liver System ver 6 0 0 Rat Genome 230 2 0 Heart System ver 3 0 0 6 In the Additional Compounds field s type the name s of any secondary compound s You can enter up to 25 characters Apostrophes are not permitted Secondary compounds are optional 7 Click Create Study 15 Study Features The Study Status Indicator for each study is updated as you progress through the phases of the workflow The indicator icons mimic those of the analysis phases on the Workflow tool bar Studies for which a pre diction has been completed display a PDF Portable Document Format icon to the right of the Study Sta tus Indicator You can access the ToxShield Suite Prediction report by clicking the PDF icon FIG 4 Study Information pane showing status indicators Study Status indicator ToxShield Suite Prediction report PDF icon TST_STUDY1 Study List TST_STUDY2 Workflow tool bar Related Topics How to Navigate Through ToxShield Suite Project Features Preparing Your Data for ToxShield Suite Analysis How to Open an Existing Study How to Edit Pro
35. u upload data from these GeneChip arrays as CEL files This section contains the following topics a What You Need to Provide a Valid File Types and Formats jenuew 13SN e1INS PIOIYSXOL Related Topics Project Features Study Features How to Select CEL Files How to Upload Selected CEL Files 2 3 1 What You Need to Provide Before you begin your ToxShield Suite session you will need the following a CEL files from a study performed on one of the supported Affymetrix GeneChip arrays Each CEL file represents a single sample run over one of these Affymetrix GeneChip arrays Rat Genome U34A Rat Genome 230 2 0 Annotations associated with the design of each study including sample name time dose and treat ment information pertaining to the vehicle and primary and secondary compound s Indication that you consider any of the included CEL files to be outliers data points that fall outside a specific range so that you can make a more accurate evaluation of the data Note You can annotate your CEL files by referring to your current study notes or you can annotate them automatically by uploading a txt text file to ToxShield Suite See also How to Annotate Your Study on page 38 Related Topics How to Prepare Study Annotation Files How to Select CEL Files How to Upload Selected CEL Files How to Annotate Your Study 19 Preparing Your Data for ToxShield Suite Analysis 2 3 2 Note
36. ult value Vehicle when either 1 the compound name does not match one of the above or 2 no value is provided Time Time of dosing provided as a number If no value is provided the Time field on the Sample Annotation page is also left blank a TimeUnit Valid time unit of dosing Currently the supported time unit is hours The TimeUnit column header must be hrs without quo tation marks Dose Sample compound dose as a character string or relative text value high medium or low If no value is provided the Dose field on the Sample Annotation page is also left blank DoseUnit Valid measure of dosing expressed as blank no value use this when your dose contains relative text values as described in Dose above mg kg 20 Working With Projects and Studies pay ml kg g kg Note Use the same DoseUnit for all samples in a given Study Related Topics Project Features Study Features jenuew 13SN e1INS PIOIYSXOL Valid File Types and Formats Study Assistant Features How to Upload Selected CEL Files 2 3 3 Valid File Types and Formats ToxShield Suite verifies that the CEL files you upload match the GeneChip array type model system you indicated when you created the Study ToxShield Suite accepts the following file types a RG U34A Version 3 ASCII and 4 binary GCOS CEL files RAE 230 2 Version 3 ASCII and 4 binary GCOS CEL files You can upload these files to To
37. xShield Suite as individual files or as a group of compressed files in a sin gle zip file You can transfer by FTP File Transfer Protocol the ASCII CEL files with either Windows or UNIX line breaks However if you transfer binary GCOS CEL files in ASCII mode via FTP before you upload them to ToxShield Suite for example if you transfer the files internally between an internal CEL file repository server and your desktop it is likely that you will corrupt the binary files Related Topics Project Features Study Features What You Need to Provide Study Assistant Features How to Upload Selected CEL Files 21 This page has been added to accomodate duplex printing
38. y multiple doses and their cor responding vehicles During the course of analyzing a Study ToxShield Suite generates refRMA Reference Robust Multi chip Average normalized expression predictive toxicogenomic modeling and compound similarity data from which it derives the compound s potential for toxicity in the study s tissue of origin Each Study you create consists of one or more compounds the primary compound under investigation and optionally up to four secondary compounds that may prove helpful in predictive analysis Secondary compounds may be similar to the primary compound in chemical structure and have known toxic effects This aspect of the study design allows you to compare side by side the toxicity scores of the primary compound with chemical s proven to be toxic In order to provide a control for any gene changes for each Study each compound s corresponding vehi cle the excipient used to dissolve the compound must be analyzed as well independent of the com pound it carries The number of model systems and generated files available to you for a Study depends on your company s con tract with Gene Logic For example you may or may not have access to the Heart Model System or marker genes If this contract should change between the time you first ran the ToxShield Suite Prediction for a given Study and the time you add or edit notes you may not be able to access certain model systems or files to which you previou
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