August 29, 2002InforMax Confidential1 Vector Xpression Product Overview

August 29, 2002 InforMax Confidential 1

Vector XpressionVector Xpression

Product OverviewProduct Overview


AgendaAgenda

• Introduction to Vector Xpression

• Product Features and Benefits

• Future Direction


AgendaAgenda





Source: BioInformatics LLC Survey 2002, InforMax Research

What do Customers Want?What do Customers Want?

• When considering bioinformatics software what When considering bioinformatics software what do Life Sciences Researchers care about most?do Life Sciences Researchers care about most?

– Intuitive and easy to use– Easy to link to external data– Strong scientific and technical support


Vector Family of ProductsVector Family of Products

Vector PathBlazerVector PathBlazerVector XpressionVector 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

VectorNTIVectorNTI


High Quality Expression ResultsHigh Quality Expression Results


Data AnalysisData AnalysisAnd MiningAnd Mining


Data AnalysisData AnalysisAnd MiningAnd Mining

INPUTS RESULTSPROCESSING

InforMax Vector Xpression leverages your InforMax Vector Xpression leverages your investment in inputs and processing to deliver to investment in inputs and processing to deliver to sophisticated analysis and high quality results.sophisticated analysis and high quality results.

ImageImageAnalysisAnalysisImageImage

AnalysisAnalysisImagingImagingImagingImagingFluidicsFluidicsFluidicsFluidicsChipsChipsChipsChipsSamplesSamplesSamplesSamples


Extracting biologically Extracting biologically meaningful meaningful information from information from microarray data microarray data requires sophisticated requires sophisticated data analysis, mining, data analysis, mining, and exploration.and exploration.

Sophisticated Analysis and MiningSophisticated Analysis and Mining



• Vector Xpression Vector Xpression is a powerful, easy to use and flexible is a powerful, easy to use and flexible application for microarray expression data analysisapplication for microarray expression data analysis

• Vector Xpression Vector Xpression makes complicated, peer-reviewed workflows makes complicated, peer-reviewed workflows easy and accessible to users of all experience levelseasy and accessible to users of all experience levels

• Vector Xpression contains a robust set of peer-reviewed Vector Xpression contains a robust set of peer-reviewed microarray gene expression analysis toolsmicroarray gene expression analysis tools

• Vector Xpression Vector Xpression is supported by experienced bioinformaticists, is supported by experienced bioinformaticists, industry leading technical support and tutorialsindustry leading technical support and tutorials

• Vector Xpression Vector Xpression is the best available software solution for both is the best available software solution for both beginners and experts in the field of microarray gene expression beginners and experts in the field of microarray gene expression analysisanalysis



• 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


AgendaAgenda





Powerful, Intuitive, FlexiblePowerful, 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


Product Features and FunctionsProduct Features and Functions

• Data Import and Storage

• Data Processing

• Data Mining and Visualization

• Link to Sequence and Pathways




• Data Processing




Database ObjectsDatabase 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)


Easy Database ManagementEasy 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.


Import data easily Import data easily and quickly using and quickly using Import WizardImport Wizard

Data in known formats imported automatically

Data Import WizardData Import Wizard

If unknown format, wizard quickly guides import


Create links to Create links to external web external web sites using User sites using User Defined FieldsDefined Fields

User Defined FieldsUser Defined Fields

Easily create Easily create and populate and populate User Defined User Defined FieldsFields


Supports:Supports:•wildcard wildcard •boolean boolean •user defined user defined fieldsfields

Database Search UtilityDatabase Search Utility


Easily import, Easily import, assign and manage assign and manage annotations based annotations based on classificationson classificationsfrom Gene Ontology from Gene Ontology ConsortiumConsortium

Annotate GenesAnnotate Genes




• Data Processing




Easy Data ProcessingEasy Data Processing

• Easy to Use Data Processing Options

– Subtract Background– Carry out Log 2 Transformations– Normalization – Filtering– Sorting


State of the art, State of the art, peer reviewed peer reviewed statistical statistical methods for methods for normalizationnormalization

• Global • Control based methods

• MA- Plot• Lowess Smoothing (global, print tip, user defined block patterns)

Pre

Post

NormalizationNormalization


Filter in many ways Filter in many ways using easy pull using easy pull down menu and down menu and dialog boxesdialog boxes

Filter OptionsFilter Options


Sort in many ways Sort in many ways using easy pull using easy pull down menu and down menu and dialog boxesdialog boxes

Sorting OptionsSorting Options




• Data Processing




Visualization OptionsVisualization 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)


Easily modify Easily modify appearance of appearance of graphicsgraphics

Customize AppearanceCustomize Appearance


Convenient layout Convenient layout for visualizing and for visualizing and analyzing analyzing expression valuesexpression values

Expression Data ViewerExpression Data Viewer


Scatter Plot Scatter Plot for easy for easy comparison comparison of two of two samplessamples

Scatter PlotScatter Plot


Easily carry out Easily carry out clustering analysis clustering analysis using several using several options and options and Cluster Validation Cluster Validation tooltool

ClusteringClustering


Convenient view Convenient view and manipulation and manipulation of cluster of cluster dendrogram dendrogram including including hierarchical two-hierarchical two-way cluster viewway cluster view

Two-way ClusteringTwo-way Clustering


Easily show Easily show and create a and create a gene profile.gene profile.

Gene ProfileGene Profile


Differential Gene ExpressionDifferential 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


Easily tag genes Easily tag genes of interest to of interest to follow through follow through analysisanalysis

Tag Genes of InterestTag Genes of Interest


View history of View history of analysis steps analysis steps performedperformed

Session HistorySession History




• Data Processing




Link to PathwaysLink to Pathways

Use Vector Pathblazer to Use Vector Pathblazer to view expression results view expression results and clusters in context and clusters in context of pathways, protein-of pathways, protein-protein interactionsprotein 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 InteractionsCo-relation Between Clustering and Protein Protein Interactions


Link to sequence analysisLink to sequence analysis

Use Vector NTI to view Use Vector NTI to view sequence record of gene sequence record of gene and run sequence and run sequence analysis toolsanalysis tools


Easily export data Easily export data to applications like to applications like Excel, MatLabExcel, MatLab

Data ExportData Export


AgendaAgenda





Continuous ImprovementContinuous 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


SummarySummary

• Vector Xpression Vector Xpression is a powerful, easy to use and flexible is a powerful, easy to use and flexible application for microarray expression data analysisapplication for microarray expression data analysis

• Vector Xpression Vector Xpression makes complicated, peer-reviewed workflows makes complicated, peer-reviewed workflows easy and accessible to users of all experience levelseasy and accessible to users of all experience levels

• Vector Xpression contains a robust set of peer-reviewed Vector Xpression contains a robust set of peer-reviewed microarray gene expression analysis toolsmicroarray gene expression analysis tools

• Vector Xpression Vector Xpression is supported by experienced bioinformaticists, is supported by experienced bioinformaticists, industry leading technical support and tutorialsindustry leading technical support and tutorials

• Vector Xpression Vector Xpression is the best available software solution for both is the best available software solution for both beginners and experts in the field of microarray gene expression beginners and experts in the field of microarray gene expression analysisanalysis


System RequirementsSystem Requirements

•Windows 98, 2000, NT, ME and XP platforms

•64MB RAM needed, 128MB recommended

•1GB HD disc space

•Internet connection


Contact Contact

Register for a tour of Vector Xpression today!

http://www.informaxinc.com/downloads.html

Documents

August 29, 2002InforMax Confidential1 Vector Xpression Product Overview