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Packard BioScience What is ArrayInformatics? Packard BioScience ARRAYINFORMATICS IS…. •An integrated software package of tools for organizing, storing and analyzing gene expression microarray data Packard BioScience DATABASE STRUCTURE REFLECTS MICROARRAY PROCESS MAP Data importation steps are identified in key microarray process areas Data process flow is based on typical microarray experiment design Data analysis and visualization is comprehensive and reproducible RESULTS Packard BioScience ArrayInformatics® Database Tools Visualization Tools Packard BioScience ArrayInformatics® Database Tools Packard BioScience ArrayInformatics Database Tools Relational database structure operating under Windows 2000 Professional and Microsoft SQL Server Stores and organizes gene expression data from QuantArray and GPR export files Direct integration with SpotArray printers, ScanArray scanners and QuantArray image analysis software Packard BioScience FLEXIBLE DATABASE WITH EASY-TO-USE INTERFACE Process Map guides data entry points Action items are specific for Process Step selected Database entries organized by Microarray Packard BioScience INTEGRATED IMPORT WITH MICROARRAY PRINTERS, SCANNERS AND ANALYSIS SOFTWARE FILES WIZARD-DRIVEN STEPS MAKE DATA IMPORT EASY AND FAST Selection of data importation step activates 5 step wizard Packard BioScience FLEXIBLE DATABASE WITH EASY-TO-USE INTERFACE Microarray data sorting and organization is done through standard column sorting functions Imported microarray data appears in database listings Packard BioScience ArrayInformatics® Visualization Tools Packard BioScience ArrayInformatics Visualization Tools Analysis Map shows each transformation for easy adjustment of entire analysis protocol Powerful graphing and clustering tools provide comprehensive data analysis Expression profile searching and matching is easy and reproducible with user-generated gene lists Easy data and graph exporting feature provides reports and publications with high quality graphics Packard BioScience EASY SELECTION OF MICROARRAYS FROM DATABASE Creating an Analysis Protocol keeps the microarrays selected from the database organized Microarrays available in the Database for analysis are listed by Experiment name Microarrays selected for analysis are transferred individually for easy organization Data Datafrom fromselected selectedmicroarrays microarrays can canbe beorganized organizedininindividual individual tabs or on a single spreadsheet tabs or on a single spreadsheet Packard BioScience INITIAL DISPLAY OF DATA IS A SPREADSHEET VIEW Packard BioScience GENE EXPRESSION MICROARRAY DATA ANALYSIS STEPS NORMALIZATION Corrects data on each individual microarray for reagent and methods variations STANDARDIZATION Corrects data across all microarrays in the analysis protocol for slide-to-slide variations FILTERING Reduces data set with user selected parameters for easier identification of actively changing gene expression patterns Packard BioScience NORMALIZATION Packard BioScience Normalization of data is a necessary transformation step Choice of Normalization methods ensures best correction for microarray variables Packard BioScience Analysis Process Map tracks Normalization step Data Node appears and will display transformation step with initial spreadsheet icon Spreadsheet icon Packard BioScience STANDARIZATION Packard BioScience Standarization across all microarrays is 2nd transformation step Data columns selected as standardization parameters are listed for easy adjustment Additional standardization methods give this step maximum flexibility All data columns are available for use as standardization parameters Packard BioScience Analysis Process Map tracks Standardization step Spreadsheet icon Data Node appears and will display transformation step with initial spreadsheet icon Packard BioScience FILTERING Packard BioScience Data filtering is a powerful 3rd transformation step (2) Selected data columns are organized for easy adjustment and changes (1) Any data column in microarray can be used as a filter (4) User-defined gene lists can be used as a powerful filtering tool (3) Filter thresholds provide flexibility and statistical power Packard BioScience Analysis Process Map tracks Filtering step Spreadsheet icon Data Node appears and will display transformation step with initial spreadsheet icon Packard BioScience GRAPHICAL VIEWS OF TRANSFORMED DATA Scatter Plot XY plot of any selected column data - typically intensity of Fluor1 vs intensity of Fluor2 Line Plot Plot of selected genes vs selected column data - typically genes vs ratio values Series Plot Plot of selected column data vs microarray time points - typically ratio values vs all selected microarrays Cluster Image Map Heat Map representation with horizontal and vertical dendrograms - typically ratio data with green (low) to red (high) Packard BioScience GRAPHICAL VIEWS OF TRANSFORMED DATA Scatter Plot XY plot of any selected column data - typically intensity of Fluor1 vs intensity of Fluor2 Line Plot Plot of selected genes vs selected column data - typically genes vs ratio values Series Plot Plot of selected column data vs microarray time points - typically ratio values vs all selected microarrays Cluster Image Map Heat Map representation with horizontal and vertical dendrograms - typically ratio data with green (low) to red (high) Packard BioScience Scatter Plot Properties & Settings Any column data can be set as X or Y axis values Any number of data rows or all data rows can be selected for display Easily adjusted threshold settings allow flexibility in viewing of ratio values indicating gene activation or suppression Packard BioScience Scatter Plot View Scatter Plot icon Packard BioScience GRAPHICAL VIEWS OF TRANSFORMED DATA Scatter Plot XY plot of any selected column data - typically intensity of Fluor1 vs intensity of Fluor2 Line Plot Plot of selected genes vs selected column data - typically genes vs ratio values Series Plot Plot of selected column data vs microarray time points - typically ratio values vs all selected microarrays Cluster Image Map Heat Map representation with horizontal and vertical dendrograms - typically ratio data with green (low) to red (high) Packard BioScience Line Plot Properties Selected rows or all rows of data can be selected for display Any single column of data or a group of columns can be selected as the pattern to plot Packard BioScience Line Plot View Specific icon appears in data node being analyzed and line plot automatically displays selected data Line Plot icon Packard BioScience GRAPHICAL VIEWS OF TRANSFORMED DATA Scatter Plot XY plot of any selected column data - typically intensity of Fluor1 vs intensity of Fluor2 Line Plot Plot of selected genes vs selected column data - typically genes vs ratio values Series Plot Plot of selected column data vs microarray time points typically ratio values vs all selected microarrays Cluster Image Map Heat Map representation with horizontal and vertical dendrograms - typically ratio data with green (low) to red (high) Packard BioScience SERIES PLOT PROPERTIES & SETTINGS Any number of rows or all rows of data in selected microarrays or all microarrays can be chosen for this plot Any data column can be selected to be plotted as the series All mnicroarrays in the series can be selected for display Packard BioScience EXPRESSION PATTERN MATCHING UTILIZES ADJUSTABLE CONFIDENCE LEVELS WITH UPPER AND LOWER THRESHOLD LIMITS Select a gene pattern by double clicking on the line of interest The selected gene pattern is displayed with upper and lower limits and correlation minimum Series Plot icon After an executed search genes with similar patterns are listed with confidence calculations RESULTING GENE LISTS PROVIDE A POWERFUL TOOL FOR DATA ANALYSIS Packard BioScience GRAPHICAL VIEWS OF TRANSFORMED DATA Scatter Plot XY plot of any selected column data - typically intensity of Fluor1 vs intensity of Fluor2 Line Plot Plot of selected genes vs selected column data - typically genes vs ratio values Series Plot Plot of selected column data vs microarray time points - typically ratio values vs all selected microarrays Cluster Image Map Heat Map representation with horizontal and vertical dendrograms - typically ratio data with green (low) to red (high) Packard BioScience POWERFUL CLUSTER IMAGE MAPS (CIM) PROVIDES COMPREHENSIVE DATA ANALYSIS Horizontal and vertical clustering with dendrograms can be independently selected Cluster Image Map Plot icon Choice of clustering algorithms ensures even a complex data set can be analyzed Packard BioScience HIEARCHICAL CLUSTERING MAP PLOT Dendrograms and heat map visualization keys enable in-depth data analysis with clustering features Packard BioScience DISPLAY CAN BE CONFIGURED FOR EASY AND FAST COMPARISONS OF DATA TRANSFORMATIONS Display can be tiled with up to 3 panes for quick and easy graphical comparisons Packard BioScience EXPORT OF ALL PLOTS IS FLEXIBLE AND EASY All plots including the CIM can be saved as Hi-Res files for use in publications and reports Packard BioScience ARRAYINFORMATICS CONFIGURATIONS Personal Edition Runs on Workstation computer 1-3 Research Edition Runs on network Server with Workstations 5-8 individual users individual users Enterprise Edition Runs on network Server with Workstations 10+ individual users Packard BioScience ARRAYINFORMATICS COMPUTER RECOMMENDATIONS Workstation (All Editions) Server (Research Edition) Pentium® III, 1GHz processor Pedistal/Tower Case 40 GB Hard Drive (One Drive, One partition formatted with NTFS) Two (2) 700 Mhz Pentium III Xeon processors or better 512 MB RAM 1 GB RAM 19” color monitor Raid Level 5 Four (4) 18 GB hard drives or better - hot swap capable Display Resolution: 1024 x 768 x 65K colors Recordable/Rewriteable CD-ROM Zip 250 disk drive 10/100 Mbs Ethernet network interface card (NIC) Recordable/Rewriteable CD-ROM 32X or better 10/100 Mbs Ethernet network interface card (NIC) 20/40 GB tape backup drive Windows 2000 Professional Server Keyboard & mouse Windows® 2000 Professional Internet Explorer 5.0 Server (Enterprise Edition) Call for information 19” Color Monitor Packard BioScience Packard BioChip Technologies is constantly making improvements to all its products including the ArrayInformatics software package. For the latest feature information on the ArrayInformatics software package contact: Packard BioChip Technologies, LLC 40 Linnell Circle Billerica, MA 01821 U.S.A. Tel: 978-439-8410 Toll Free: 1-888-323-9681 Fax: 978-439-8430 Web site: http://www.packardbioscience.com E-mail: [email protected] E-mail technical services: [email protected] For all international representatives, contact the Packard BioScience U.S.A. office Packard BioScience A POWERFUL EASY-TO-USE SOLUTION TO YOUR MICROARRAY DATA STORAGE AND ANALYSIS NEEDS Packard BioScience