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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
Technologies For Genome Wide Analysis
Gene
Genome
Transcriptome
Transcript
Protein
Proteome
Key Components of Expression Databases
Incyte has the key components
4,645,958 Sequences
>1500 CPU PC-Farm
109,938 human Genes
(5’-3’ confirmed)
>75 Terabytes of capacity
Software
Genes
GEM™ cDNA
Microarrays
Data Management
Toxicology
Drug profiles
Pathway analysis
Disease tissues
Normal tissues
Proteomics
10,000 genes per GEM
Proteomics Databases
>100,000 genes on GEMs
HTP technology with OGS
19 different GEMs in total
Matched RNA/Protein Exp.
Incyte’s Expression Databases Support
Target Discovery and Lead Optimization
Target Discovery Lead Discovery and Optimization
Primary Secondary
Screening Screening
Protein
Screen
Dev.
RNA
RNA
Protein
Target
Seln.
Target
Idn.
Lead
Optn.
Make-Test
Cycle
“Accelerating Selection “Accelerating Compound Selection and
Decreasing the Attrition Rate”
of High Quality Targets ”
Gene Expression Databases Require
Integration
Analytical Tools
Integrated
DB
Proprietary
Data
Non-Proprietary
Data
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
Microarray Data
Management and Analysis
• 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
Data Management
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Clinical and experiment information
Sample preparation
Hybridization conditions
Genes/clones/sequences
Expression values
Summarization/Normalization Methods
Microarray Design
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
RDBMS
Database
Loader
PMD
File
PMD
Driver
Raw Data
File
• Requires no knowledge
of database structure
• Minimize need for enduser to change software
when schema changes
are required
• No knowledge of userspecific systems
required
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