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FDA/NCTR Toxicoinformatics Workshop: "
Toxicogenomics Database, Study Design and Data Analysis",
Wednesday, December 4, 2002
Objectives: A highly interactive gathering
of a small group of individuals with a strong interest in toxicoinformatics for
microarray experiments. The workshop focused on
"practical" issues that are critical for successful application of microarrays
in the toxicological sciences.
- Experiment Design – From a statistical and/or biological
perspective, what are the issues and strategies necessary to design a valid
experiment for dose-response study, disease-stage differentiation, and
biomarker identification?
- Normalization and Statistical Analysis – What options are available
and are they adequate? Is standardization and automation possible?
- Microarray Database – How should the MIAME standard be implemented
for toxicology studies? What should be QA/QC for a validated database where
data is entered only by meeting prescribed standards for completeness,
accuracy, normalization and conformance to the applicable ontology?
- Toxicogenomics Infrastructure – Which public genomic and pathway
sources should be integrated with microarray data for the toxicology community
and what strategies are needed for integration? What other chemical,
pathological and toxicological sources should be integrated? Are we ready for
the integration of microarray data with proteomics and metabonomics data? If
yes, what level of integration is expected? What visualization and data
analysis approaches should be included to provide toxicogenomics capability?
Speakers
Morning Sessions - Microarray Study Design and Data
Analysis
- Opening Remarks, Daniel Casciano, Ph.D., Director of NCTR, FDA
(PowerPoint
slides 320KB)
- Introduction, Ralph Kodell, Ph.D., Division Director of Biometry and Risk
Assessment, NCTR, FDA (PowerPoint
slides 13KB)
- Putting the Genome Back Into Functional Genomics, John Quackenbush,
Ph.D.,The Institute for Genomic Research (TIGR) (PowerPoint
slides 14390KB)
- Figures of Merit for Evaluating Different Data Analysis Methods and
Experiment Design, Yudong He, Ph.D., Rosetta Inpharmatics, Inc
(PowerPoint
slides 4186KB)
- Design of Functional Genomic Studies that Measure Gene Expression with
Microarrays, Robert Delongchamp, Ph.D., NCTR (pdf)
- Panel Discussion, Moderator: Cheryl Walker, Ph.D., MD Anderson Cancer
Center, University of Texas
Afternoon Sessions - Microarray Database and
Toxicogenomics Infrastructure
- Introduction, Jim Fuscoe, Ph.D., Program Director of Center for Functional
Genomics, NCTR, FDA (PowerPoint
slides 26KB)
- ArrayTrack - Supporting Microarray Studies through Data Integration, Weida
Tong, Ph.D., NCTR, FDA (PowerPoint
slides 3824KB)
- A Database Centric Approach for Analyzing the Influence of Environmental
Perturbations on Phenotypic traits, Jeff Blanchard, Ph.D., National Center for
Genome Resources (PowerPoint
slides 3586KB)
- Development of a Relational Toxicogenomics Database for the Prediction of
Chemical Toxicity, Lyle Burgoon, Ph.D., Michigan State University
(PowerPoint
slides 1222KB)
- Building a Flexible Data Management Infrastructure with DiscoveryLink,
Paul Brake, Ph.D., IBM (PowerPoint
slides 2264KB)
- Panel Discussion, Moderator: Michael Waters, Ph.D., Assistant Director for
Database Development, NIEHS / NCT
- Closing Remarks, Roger Ulrich, Ph.D., Senior Scientific Director, Rosetta
Inpharmatics, Inc.
Organizers:
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