1. Copyright 2000, Media Cybernetics, L.P. Array-Pro ® Analyzer Software

2. Copyright 2000, Media Cybernetics, L.P. Problems with Current Array Analysis Tedious manual application of grid templates Non-reproducibility from one user to another or the same user doing a similar analysis on another sample Poor user feedback on image and hybridization quality Poor signal/noise performance due to lack of understanding of signal/background

3. Copyright 2000, Media Cybernetics, L.P. Goals for Array-Pro Automate grid/spot finding based on our superior knowledge of image processing; find regular & irregular array spotting Allow manual setup but let the computer make decisions whenever possible for reproducibility Give the user constant feedback in processing and data to aid their assessment of array and spot quality Use our experience in image processing to optimize signal/noise performance Read existing file formats (mostly TIFF) Drive confocal microscopes with automation to collect images

4. Copyright 2000, Media Cybernetics, L.P. Application Goals Ability to generate information from all kinds of arrays –Spotted arrays –Gene chips (e.g. Affymetrix) –Membranes (e.g. Clontech Atlas, Research Genetics) Especially well-suited for gene expression –Ratios (usually Cy3/Cy5) –Scatter plots, tables, color-coded graphics, etc. to expose gene expression

5. Copyright 2000, Media Cybernetics, L.P. Experiment Driven

6. Copyright 2000, Media Cybernetics, L.P. Spot ID Wizard

7. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

8. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

9. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

10. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

11. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

12. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

13. Copyright 2000, Media Cybernetics, L.P. Wizard Continued

14. Copyright 2000, Media Cybernetics, L.P. Auto Grid/Spot Detection Parameters

15. Copyright 2000, Media Cybernetics, L.P. Advanced Detection

16. Copyright 2000, Media Cybernetics, L.P. Numerous Measurements/Descriptors

17. Copyright 2000, Media Cybernetics, L.P. Analysis Options

18. Copyright 2000, Media Cybernetics, L.P. Labeling

19. Copyright 2000, Media Cybernetics, L.P. Background Characterization

20. Copyright 2000, Media Cybernetics, L.P. Information View Definition

21. Copyright 2000, Media Cybernetics, L.P. ID and Replication

22. Copyright 2000, Media Cybernetics, L.P. Grid Labeling Options

23. Copyright 2000, Media Cybernetics, L.P. Data Tables

24. Copyright 2000, Media Cybernetics, L.P. Statistical Feedback

25. Copyright 2000, Media Cybernetics, L.P. Data Histograms

26. Copyright 2000, Media Cybernetics, L.P. Cell Group Information

27. Copyright 2000, Media Cybernetics, L.P. Scatter Plot

28. Copyright 2000, Media Cybernetics, L.P. Other Features Floating windows of information over cells in image Label importing Definition of groups, including fiducials, background, housekeeping genes, outliers, etc. Interactivity of data and graphics Working with spots or user-defined groups of spots Image & hybridization quality metrics; user weighted Scope-Pro as a plug-in module to automate microscope stages Database storage

29. Copyright 2000, Media Cybernetics, L.P. Partnership with Applied Maths Array-Pro shares data seamlessly with GeneMaths ® Can start GeneMaths from Array-Pro and pass experiment data automatically Sophisticated statistical analysis of experimental series data

30. Copyright 2000, Media Cybernetics, L.P. GeneMaths ® Standardization of data matrix using offset and scaling functions (averages, Root Mean Square, Standard Deviation) Transformation of data matrix (flipping) Powerful two-way cluster analysis of rows and columns using a variety of similarity/distance coefficients, and several pair-group clustering methods, Ward, and Neighbor Joining Cluster significance indication based on bootstrap techniques Very powerful dendrogram layout and visualization tools to facilitate interpretation of analyses of extreme sizes Use and display up to 20 database fields both for rows and columns Advanced search and select functions based upon database information Pattern matching: search for closest matches with specific profiles, average profiles or theoretical profiles Single, composite or average profile curve or bar graph plotting with indication of standard deviations X-Y plots, time course plots, and scatterplots; 2-D and 3-D Principal Component Analysis and Discriminant Analysis with or without variance Advanced Self-Organizing maps (Kohonen maps) of any size with unique presentation and interpretation tools; Powerful WYSIWYG printing of any result.

31. Copyright 2000, Media Cybernetics, L.P. GeneMaths ®

32. Copyright 2000, Media Cybernetics, L.P. GeneMaths ®