Expression Data Integration Microarray Gene Expression Database Meeting Sunday 14th November 1999

Key Topics Incyte’s experience with expression databases The need for integrated data management and analysis A technology-independent exchange format for expression data

Transcript Genome Transcriptome Proteome Gene Protein Technologies For Genome Wide Analysis

Key Components of Expression Databases Genes 4,645,958 Sequences 109,938 human Genes (5’-3’ confirmed) GEM™ cDNA Microarrays 10,000 genes per GEM >100,000 genes on GEMs 19 different GEMs in total Normal tissues Disease tissues Drug profiles Toxicology Pathway analysis Data Management >1500 CPU PC-Farm >75 Terabytes of capacity Software Proteomics Databases HTP technology with OGS Matched RNA/Protein Exp. Proteomics Incyte has the key components

Incyte’s Expression Databases Support Target Discovery and Lead Optimization Target Id n. Target Sel n. Screen Dev. Primary Screening Secondary Screening Lead Opt n. Target DiscoveryLead Discovery and Optimization Make-Test Cycle “Accelerating Selection of High Quality Targets ” “ Accelerating Compound Selection and Decreasing the Attrition Rate” RNA Protein RNA Protein

Integrated DB Proprietary Data Non-Proprietary Data Analytical Tools Gene Expression Databases Require Integration

The rate of change in microarray technology will accelerate from major impact players entering the marketplace Current players Incyte Affymetrix NEN Clonetech Emerging Players Motorola Hewlett-Packard Perkin-Elmer Amersham Corning Roche

Technology-independent: Can store and analyze data from any microarray technology (single or dual channel) Provides tools to allow users to load their own microarray data into the database Microarray Data Management and Analysis

Clinical and experiment information Sample preparation Hybridization conditions Genes/clones/sequences Expression values Summarization/Normalization Methods Microarray Design Data Management

Analytical Tools Query on most database attributes Average hybridizations; Composite hybridizations Data visualization Clustering Sequence analysis User-defined gene groups Data export; Spotfire™ integration Links to Incyte and PD databases

Take-home message: Central to the successful creation of an expression community will be the ratification of a common data exchange protocol and format.

LifeArray™ Data Import Requires no knowledge of database structure Minimize need for end- user to change software when schema changes are required No knowledge of user- specific systems required Raw Data File PMD Driver RDBMS PMD File Database Loader

Combining the Power of PMD with the Extensibility of XML Why XML? XML: Extensible Markup Language W3C Standard: V1.0, Feb 1998 Powerful language for defining custom markup languages Well suited for PMD content DTD DB