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Allan Peter Davis Scientific Curator The Mount Desert Island Biological Laboratory

Curating the Comparative Toxicogenomics Database : a knowledge and discovery environment for chemical-gene-disease associations. Allan Peter Davis Scientific Curator The Mount Desert Island Biological Laboratory Salisbury Cove, Maine. GENES. DNA Repair. Cell Cycle Control. Phenotype.

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Allan Peter Davis Scientific Curator The Mount Desert Island Biological Laboratory

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  1. Curating the Comparative Toxicogenomics Database:a knowledge and discovery environment for chemical-gene-disease associations Allan Peter Davis Scientific Curator The Mount Desert Island Biological Laboratory Salisbury Cove, Maine

  2. GENES DNA Repair Cell Cycle Control Phenotype Environment Cell Death/ Differentiation Distribution/ Metabolism CHEMICAL DISEASE Chemical exposure is a significant environmental factor for health DISEASE

  3. Chemicals 59,000 Genes >30,000 Diseases 20,000 Papers 80,000 Discover information CTD facilitates knowledge and discovery by integrating data http://ctd.mdibl.org

  4. Curating the chemical-gene-disease triad C chemical-gene interactions chemical-disease associations G gene-disease associations

  5. Curating the chemical-gene-disease triad CONTROLLED VOCABULARIES C MeSH chemical-gene interactions chemical-disease associations 65 2 Entrez-Taxon G gene-disease associations Entrez-Gene 2 MeSH

  6. Analog Metabolite Increase Decrease No effect Binds Activity Expression Transport - Uptake - Import - Secretion - Export Metabolic processing - Degradation - Chemical synthesis - Methylation - Oxidation - Phosphorylation - Ubiquitination plus lots more… Protein DNA - promoter - enhancer - exon - intron mRNA - 5’ UTR - 3’ UTR - polyA tail Modified form Alternative form Mutant form - polymorphism - SNP Species Curating the chemical-gene branch C G

  7. Curating the disease branch: 2 sources C Mechanism / marker Therapeutic / target G 1. 2.

  8. User-friendly query pages Query for Chemicals, Genes, Interactions, Diseases, or References each query page can be refined with additional parameters Q: what enzymes have their expression affected by cadmium exposure?

  9. Explore CTD via Chemical, Gene, or Disease pages

  10. GENE: Basic Information tab Data tabs

  11. GENE: Chemicals tab Sort columns by clicking on headers Ranked by number of curated interactions

  12. Download results onto desktop GENE: Interactions tab Sort columns by clicking on headers

  13. ABCB11 CHOLESTASIS GENE: Disease tab Direct gene- disease association

  14. GENE: Disease tab Discover novel, putative disease connections ABCB11 Estradiol PROSTATE CANCER Estradiol inferred

  15. G C C G C G Discover putative chemical-gene-disease networks 738 chemicals linked to LUNG CANCER via gene intermediate 1426 genes linked to LUNG CANCER via chemical intermediate

  16. my house! CTD evaluation: arsenic as a case study • Natural and man-made sources (e.g., pesticides & fertilizers) • Top environmental health threat worldwide • Associated with numerous diseases • Mechanisms of action - unknown Use CTD to find putative molecular mechanisms of arsenic exposure

  17. As 1437 genes Transcription factor Cell cycle, proliferation, apoptosis Stress response protein regulated by numerous transcription factors

  18. As 1437 408 Can CTD predict diseases caused by As exposure? inferred As diseases Cancer Skin Digestive Neurological Metabolic Immune Urogenital Poisoning Blood Endocrine Cardiovascular Musculoskeletal Respiratory Mental disorders

  19. inferred As diseases Cancer Skin Digestive Neurological Metabolic Immune Urogenital Poisoning Blood Endocrine Cardiovascular Musculoskeletal Respiratory Mental disorders As 1437 408 Can CTD predict diseases caused by As exposure? Interesting parallel known As diseases Cancer Skin lesions Digestive Cardiovascular Neurological Respiratory Immune Endocrine Blood

  20. inferred As diseases Cancer Skin Digestive Neurological Metabolic Immune Urogenital Poisoning Blood Endocrine Cardiovascular Musculoskeletal Respiratory Mental disorders Leveraging arsenic-gene-disease curation

  21. CTD: a knowledge and discovery environment K N O W L E D G E D I S C O V E R Y

  22. Principal Investigators Carolyn Mattingly Scientific Curators Allan Peter Davis Cindy Murphy Scientific Software Engineers Michael Rosenstein Thomas Wiegers System Administrator Roy McMorran Funding NIEHS (ES014065 and ES003828) NCRR (RR016463) CTD Team http://ctd.mdibl.org

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