FDA Logo Link U.S. Food and Drug AdministrationNational Center for Toxicological Research
U.S. Department of Health and Human Services
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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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