1. Packard BioScience

2. Packard BioScience What is ArrayInformatics?

3. Packard BioScience An integrated software package of tools for organizing, storing and analyzing gene expression microarray data ARRAYINFORMATICS IS….

4. 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 RESULTS Data analysis and visualization is comprehensive and reproducible

5. Packard BioScience ArrayInformatics® Database Tools Visualization Tools

6. Packard BioScience ArrayInformatics® Database Tools

7. 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

8. Packard BioScience FLEXIBLE DATABASE WITH EASY-TO-USE INTERFACE Process Map guides data entry points Process Map guides data entry points Action items are specific for Process Step selected Action items are specific for Process Step selected Database entries organized by Microarray Database entries organized by Microarray

9. Packard BioScience INTEGRATED IMPORT WITH MICROARRAY PRINTERS, SCANNERS AND ANALYSIS SOFTWARE FILES WIZARD-DRIVEN STEPS MAKE DATA IMPORT EASY AND FAST 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 Selection of data importation step activates 5 step wizard

10. Packard BioScience FLEXIBLE DATABASE WITH EASY-TO-USE INTERFACE Microarray data sorting and organization is done through standard column sorting functions Microarray data sorting and organization is done through standard column sorting functions Imported microarray data appears in database listings Imported microarray data appears in database listings

11. Packard BioScience ArrayInformatics ® Visualization Tools

12. 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

13. Packard BioScience EASY SELECTION OF MICROARRAYS FROM DATABASE Creating an Analysis Protocol keeps the microarrays selected from the database organized 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 available in the Database for analysis are listed by Experiment name Microarrays selected for analysis are transferred individually for easy organization Microarrays selected for analysis are transferred individually for easy organization Data from selected microarrays can be organized in individual tabs or on a single spreadsheet Data from selected microarrays can be organized in individual tabs or on a single spreadsheet Data from selected microarrays can be organized in individual tabs or on a single spreadsheet Data from selected microarrays can be organized in individual tabs or on a single spreadsheet

14. Packard BioScience INITIAL DISPLAY OF DATA IS A SPREADSHEET VIEW

15. Packard BioScience GENE EXPRESSION MICROARRAY DATA ANALYSIS STEPS 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 NORMALIZATION  Corrects data on each individual microarray for reagent and methods variations

16. Packard BioScience NORMALIZATION

17. Packard BioScience Normalization of data is a necessary transformation step Choice of Normalization methods ensures best correction for microarray variables Choice of Normalization methods ensures best correction for microarray variables

18. Packard BioScience Analysis Process Map tracks Normalization step Data Node appears and will display transformation step with initial spreadsheet icon Data Node appears and will display transformation step with initial spreadsheet icon Spreadsheet icon Spreadsheet icon

19. Packard BioScience STANDARIZATION

20. Packard BioScience Standarization across all microarrays is 2nd transformation step All data columns are available for use as standardization parameters All data columns are available for use as standardization parameters Data columns selected as standardization parameters are listed for easy adjustment Data columns selected as standardization parameters are listed for easy adjustment Additional standardization methods give this step maximum flexibility Additional standardization methods give this step maximum flexibility

21. Packard BioScience Analysis Process Map tracks Standardization step Data Node appears and will display transformation step with initial spreadsheet icon Data Node appears and will display transformation step with initial spreadsheet icon Spreadsheet icon Spreadsheet icon

22. Packard BioScience FILTERING

23. Packard BioScience Data filtering is a powerful 3rd transformation step (1) Any data column in microarray can be used as a filter (1) Any data column in microarray can be used as a filter (2) Selected data columns are organized for easy adjustment and changes (2) Selected data columns are organized for easy adjustment and changes (3) Filter thresholds provide flexibility and statistical power (3) Filter thresholds provide flexibility and statistical power (4) User-defined gene lists can be used as a powerful filtering tool (4) User-defined gene lists can be used as a powerful filtering tool

24. Packard BioScience Analysis Process Map tracks Filtering step Data Node appears and will display transformation step with initial spreadsheet icon Data Node appears and will display transformation step with initial spreadsheet icon Spreadsheet icon Spreadsheet icon

25. 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)

26. 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)

27. Packard BioScience Scatter Plot Properties & Settings Any column data can be set as X or Y axis values 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 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 Easily adjusted threshold settings allow flexibility in viewing of ratio values indicating gene activation or suppression

28. Packard BioScience Scatter Plot View Scatter Plot icon Scatter Plot icon

29. 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)

30. Packard BioScience Line Plot Properties Selected rows or all rows of data can be selected for display 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 Any single column of data or a group of columns can be selected as the pattern to plot

31. Packard BioScience Specific icon appears in data node being analyzed and line plot automatically displays selected data Specific icon appears in data node being analyzed and line plot automatically displays selected data Line Plot View Line Plot icon Line Plot icon

32. 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)

33. 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 number of rows or all rows of data in selected microarrays or all microarrays can be chosen for this plot All mnicroarrays in the series can be selected for display All mnicroarrays in the series can be selected for display Any data column can be selected to be plotted as the series Any data column can be selected to be plotted as the series

34. Packard BioScience RESULTING GENE LISTS PROVIDE A POWERFUL TOOL FOR DATA ANALYSIS 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 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 The selected gene pattern is displayed with upper and lower limits and correlation minimum After an executed search genes with similar patterns are listed with confidence calculations After an executed search genes with similar patterns are listed with confidence calculations Series Plot icon Series Plot icon

35. 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)

36. Packard BioScience POWERFUL CLUSTER IMAGE MAPS (CIM) PROVIDES COMPREHENSIVE DATA ANALYSIS Choice of clustering algorithms ensures even a complex data set can be analyzed Choice of clustering algorithms ensures even a complex data set can be analyzed Horizontal and vertical clustering with dendrograms can be independently selected Horizontal and vertical clustering with dendrograms can be independently selected Cluster Image Map Plot icon Cluster Image Map Plot icon

37. Packard BioScience Dendrograms and heat map visualization keys enable in-depth data analysis with clustering features Dendrograms and heat map visualization keys enable in-depth data analysis with clustering features HIEARCHICAL CLUSTERING MAP PLOT

38. 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 Display can be tiled with up to 3 panes for quick and easy graphical comparisons

39. Packard BioScience All plots including the CIM can be saved as Hi-Res files for use in publications and reports All plots including the CIM can be saved as Hi-Res files for use in publications and reports EXPORT OF ALL PLOTS IS FLEXIBLE AND EASY

40. Packard BioScience ARRAYINFORMATICS CONFIGURATIONS Personal Edition  Runs on Workstation computer  1-3 individual users Research Edition  Runs on network Server with Workstations  5-8 individual users Enterprise Edition  Runs on network Server with Workstations  10+ individual users

41. Packard BioScience ARRAYINFORMATICS COMPUTER RECOMMENDATIONS Workstation (All Editions)  Pentium ® III, 1GHz processor  40 GB Hard Drive (One Drive, One partition formatted with NTFS)  512 MB RAM  19” color monitor  Display Resolution: 1024 x 768 x 65K colors  Recordable/Rewriteable CD-ROM  Zip 250 disk drive  10/100 Mbs Ethernet network interface card (NIC)  Windows ® 2000 Professional  Internet Explorer 5.0 Server (Research Edition)  Pedistal/Tower Case  Two (2) 700 Mhz Pentium III Xeon processors or better  1 GB RAM  Raid Level 5  Four (4) 18 GB hard drives or better - hot swap capable  19” Color Monitor  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 Server (Enterprise Edition)  Call for information

42. 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: 978-439-8410Toll Free: 1-888-323-9681 Fax: 978-439-8430Web site: http://www.packardbioscience.com E-mail: array@packardbioscience.com E-mail technical services: pbtsupport@packardbioscience.com For all international representatives, contact the Packard BioScience U.S.A. office Packard BioChip Technologies, LLC 40 Linnell Circle Billerica, MA 01821 U.S.A. Tel: 978-439-8410Toll Free: 1-888-323-9681 Fax: 978-439-8430Web site: http://www.packardbioscience.com E-mail: array@packardbioscience.com E-mail technical services: pbtsupport@packardbioscience.com For all international representatives, contact the Packard BioScience U.S.A. office

43. Packard BioScience A POWERFUL EASY-TO-USE SOLUTION TO YOUR MICROARRAY DATA STORAGE AND ANALYSIS NEEDS