1. August 29, 2002InforMax Confidential1 Vector Xpression Product Overview

2. August 29, 2002InforMax Confidential2Agenda Introduction to Vector Xpression Product Features and Benefits Future Direction

3. August 29, 2002InforMax Confidential3Agenda Introduction to Vector Xpression Product Features and Benefits Future Direction

4. August 29, 2002InforMax Confidential4 Source: BioInformatics LLC Survey 2002, InforMax Research What do Customers Want? When considering bioinformatics software what do Life Sciences Researchers care about most?When considering bioinformatics software what do Life Sciences Researchers care about most? –Intuitive and easy to use –Easy to link to external data –Strong scientific and technical support

5. August 29, 2002InforMax Confidential5 Vector Family of Products Vector PathBlazer Vector Xpression Work with RNA quantitation Which genes are turned on or off under conditions of interest Gene and sample profiling Work with biological pathways and protein- protein interactions Add your own data to curated data Work with gene and protein sequence Understand sequence Classify genes based on sequence similarity Design sequences for wet lab experiments VectorNTI

6. August 29, 2002InforMax Confidential6 High Quality Expression Results Vector Xpression Vector Xpression Data Analysis And Mining Vector Xpression Vector Xpression Data Analysis And Mining INPUTSRESULTSPROCESSING InforMax Vector Xpression leverages your investment in inputs and processing to deliver to sophisticated analysis and high quality results. ImageAnalysisImageAnalysisImagingImagingFluidicsFluidicsChipsChipsSamplesSamples

7. August 29, 2002InforMax Confidential7 Extracting biologically meaningful information from microarray data requires sophisticated data analysis, mining, and exploration. Sophisticated Analysis and Mining

8. August 29, 2002InforMax Confidential8 Vector Xpression Vector Xpression is a powerful, easy to use and flexible application for microarray expression data analysisVector Xpression is a powerful, easy to use and flexible application for microarray expression data analysis Vector Xpression makes complicated, peer-reviewed workflows easy and accessible to users of all experience levelsVector Xpression makes complicated, peer-reviewed workflows easy and accessible to users of all experience levels Vector Xpression contains a robust set of peer-reviewed microarray gene expression analysis toolsVector Xpression contains a robust set of peer-reviewed microarray gene expression analysis tools Vector Xpression is supported by experienced bioinformaticists, industry leading technical support and tutorialsVector Xpression is supported by experienced bioinformaticists, industry leading technical support and tutorials Vector Xpression is the best available software solution for both beginners and experts in the field of microarray gene expression analysisVector Xpression is the best available software solution for both beginners and experts in the field of microarray gene expression analysis

9. August 29, 2002InforMax Confidential9 Vector Xpression Powerful Features –Easy data import wizard accommodates almost any format –Local storage and management of microarray expression data –Data analysis using a comprehensive set of state of the art, peer-reviewed methods Focused on User Needs –Ease of use (intuitive GUI, tutorials and industry leading support) –Compelling core functionality (sophisticated, peer reviewed, data processing and analysis methods) –Links with other applications (Sequence and Pathways) –Configurable links to biological databases and GO annotations –Backed by InforMax Global Services and Technical Support

10. August 29, 2002InforMax Confidential10Agenda Introduction to Vector Xpression Product Features and Benefits Future Direction

11. August 29, 2002InforMax Confidential11 Powerful, Intuitive, Flexible Simple wizard to import data in any format User defined fields to extend data model Easy background correction and log ratio transformation Variety of ways to filter and sort data. Gene profiling and statistical validation for differential gene expression Comprehensive set of advanced, peer reviewed statistical methods and clustering algorithms with choice of several distance metric comparison options and cluster validation Easy link to sequence analysis application (Vector NTI) and pathways application (Vector PathBlazer) Import and incorporate annotations from GO consortium Easily configurable external links to biological databases

12. August 29, 2002InforMax Confidential12 Product Features and Functions Data Import and Storage Data Processing Data Mining and Visualization Link to Sequence and Pathways

13. August 29, 2002InforMax Confidential13 Product Features and Functions Data Import and Storage Data Processing Data Mining and Visualization Link to Sequence and Pathways

14. August 29, 2002InforMax Confidential14 Database Objects Expression Genes (Probes) Expression runs (Hybridizations) Expression Targets (Samples) Experiments (related hybridizations) Physical Chips (Chip layout) Run Projects (organize experiments to be analyzed) Raw data (original data from image analysis)

15. August 29, 2002InforMax Confidential15 Easy Database Management Utilities Select Database Opens an Expression database other than the default. This allows you to have several different databases to work with and to alternately view those databases. Database Compact Removes from the data files and database tables any unnecessary data that may accumulate from extensive creation and deletion of database objects. New Empty Database Creates a new and empty expression database. This option is useful when your current database become very large, or when you have a large number of database objects in a specific project.

16. August 29, 2002InforMax Confidential16 Import data easily and quickly using Import Wizard Data in known formats imported automatically Data Import Wizard If unknown format, wizard quickly guides import

17. August 29, 2002InforMax Confidential17 Create links to external web sites using User Defined Fields User Defined Fields Easily create and populate User Defined Fields

18. August 29, 2002InforMax Confidential18 Supports: wildcardwildcard booleanboolean user defined fieldsuser defined fields Database Search Utility

19. August 29, 2002InforMax Confidential19 Easily import, assign and manage annotations based on classifications from Gene Ontology Consortium Annotate Genes

20. August 29, 2002InforMax Confidential20 Product Features and Functions Data Import and Storage Data Processing Data Mining and Visualization Link to Sequence and Pathways

21. August 29, 2002InforMax Confidential21 Easy Data Processing Easy to Use Data Processing Options –Subtract Background –Carry out Log 2 Transformations –Normalization –Filtering –Sorting

22. August 29, 2002InforMax Confidential22 State of the art, peer reviewed statistical methods for normalization Global Control based methods MA- Plot Lowess Smoothing (global, print tip, user defined block patterns) Pre PostNormalization

23. August 29, 2002InforMax Confidential23 Filter in many ways using easy pull down menu and dialog boxes Filter Options

24. August 29, 2002InforMax Confidential24 Sort in many ways using easy pull down menu and dialog boxes Sorting Options

25. August 29, 2002InforMax Confidential25 Product Features and Functions Data Import and Storage Data Processing Data Mining and Visualization Link to Sequence and Pathways

26. August 29, 2002InforMax Confidential26 Visualization Options Graphics –Scatter plot –Histogram –MA-plot –Quartile plot –Bootstrap confidence plot –Several model checking plots –Hierachical biclustering (simultaneous view of clustering of samples and genes)

27. August 29, 2002InforMax Confidential27 Easily modify appearance of graphics Customize Appearance

28. August 29, 2002InforMax Confidential28 Convenient layout for visualizing and analyzing expression values Expression Data Viewer

29. August 29, 2002InforMax Confidential29 Scatter Plot for easy comparison of two samples Scatter Plot

30. August 29, 2002InforMax Confidential30 Easily carry out clustering analysis using several options and Cluster Validation tool Clustering

31. August 29, 2002InforMax Confidential31 Convenient view and manipulation of cluster dendrogram including hierarchical two- way cluster view Two-way Clustering

32. August 29, 2002InforMax Confidential32 Easily show and create a gene profile. Gene Profile

33. August 29, 2002InforMax Confidential33 Differential Gene Expression State of the art and peer-reviewed methods for validation –t- test statistic –Step down method for Multiple testing –Latin Squares (ANOVA) / Dye swap

34. August 29, 2002InforMax Confidential34 Easily tag genes of interest to follow through analysis Tag Genes of Interest

35. August 29, 2002InforMax Confidential35 View history of analysis steps performed Session History

36. August 29, 2002InforMax Confidential36 Product Features and Functions Data Import and Storage Data Processing Data Mining and Visualization Link to Sequence and Pathways

37. August 29, 2002InforMax Confidential37 Link to Pathways Use Vector Pathblazer to view expression results and clusters in context of pathways, protein- protein interactions “When you find a coincidence between RNAs that co-cluster and proteins that interact, it... reinforces your confidence that they're both correct." George Church, Harvard Medical School, The Scientist Source: H. Ge et al., "Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae," Nature Genetics, 29:482-6, December 2001 Co-relation Between Clustering and Protein Protein Interactions

38. August 29, 2002InforMax Confidential38 Link to sequence analysis Use Vector NTI to view sequence record of gene and run sequence analysis tools

39. August 29, 2002InforMax Confidential39 Easily export data to applications like Excel, MatLab Data Export

40. August 29, 2002InforMax Confidential40Agenda Introduction to Vector Xpression Product Features and Benefits Future Direction

41. August 29, 2002InforMax Confidential41 Continuous Improvement Powerful, Intuitive, Flexible –Wizard based workflow guides based on popular peer reviewed papers –Collaborative data sharing (workgroup) –Scriptability and automation –Ability to call plug-ins written in commonly used scripting languages –Open architecture allowing easy customization –Keep up with evolving microarray technology –Keep up with RNA, protein expression measurement technologies

42. August 29, 2002InforMax Confidential42Summary Vector Xpression is a powerful, easy to use and flexible application for microarray expression data analysisVector Xpression is a powerful, easy to use and flexible application for microarray expression data analysis Vector Xpression makes complicated, peer-reviewed workflows easy and accessible to users of all experience levelsVector Xpression makes complicated, peer-reviewed workflows easy and accessible to users of all experience levels Vector Xpression contains a robust set of peer-reviewed microarray gene expression analysis toolsVector Xpression contains a robust set of peer-reviewed microarray gene expression analysis tools Vector Xpression is supported by experienced bioinformaticists, industry leading technical support and tutorialsVector Xpression is supported by experienced bioinformaticists, industry leading technical support and tutorials Vector Xpression is the best available software solution for both beginners and experts in the field of microarray gene expression analysisVector Xpression is the best available software solution for both beginners and experts in the field of microarray gene expression analysis

43. August 29, 2002InforMax Confidential43 System Requirements Windows 98, 2000, NT, ME and XP platforms 64MB RAM needed, 128MB recommended 1GB HD disc space Internet connection

44. August 29, 2002InforMax Confidential44Contact Register for a tour of Vector Xpression today! http://www.informaxinc.com/downloads.html