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TG Gates: a large-scale transcriptomics and pathology database

TG Gates: a large-scale transcriptomics and pathology database. Florian Caiment. National Projects of Toxicogenomics in Japan (TGP). Toxicogenomics Project / TGP (2002-2007) National Institute of Health Science (NIHS) National Institute of Biomedical Innovation

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TG Gates: a large-scale transcriptomics and pathology database

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  1. TG Gates: a large-scale transcriptomics and pathology database Florian Caiment

  2. National Projects of Toxicogenomics in Japan (TGP) • Toxicogenomics Project / TGP (2002-2007) • National Institute of Health Science (NIHS) • National Institute of Biomedical Innovation • 15 Japanese pharmaceutical companies • Generating data for toxicology: • Compounds • Rat and human • in vivo and in vitro • liver and kidney • different doses • different exposure duration • single dose and repetitive dose

  3. National Projects of Toxicogenomics in Japan (TGP) • Toxicogenomics Genomics-Assisted Toxicity Evaluation system : TG_Gates • Approximately 170 compounds (both of in-vivo and in-vitro) • clinical, pathological and expression data • >20,000 microarray profiles (Affymetrix GeneChip)

  4. National Projects of Toxicogenomics in Japan 2 (TGP2) • TGP2 (2007-2012): Developing biomarker for : • desease diagnosis • predicting compound toxicity • Publications available on : • hepatotoxicity • phospholipidosis • coagulopathy • acetaminophen toxicity • chemical-induced glutathione depletion • ...

  5. http://toxico.nibio.go.jp/

  6. Compound list

  7. Data quality • inter and intra-laboratory reproducibility of the replicates by: • Clustering • Spearman correlation • Overlap in lists of DE genes

  8. Data quality

  9. Toxygates http://targetmine.nibio.go.jp:8080/otgviewer/

  10. Toxygates

  11. Toxygates

  12. Toxygates

  13. Toxygates

  14. Toxygates

  15. Toxygates

  16. Conclusion • Huge open access toxicogenomics dataset • Liver and Kidney • In vivo (rat) and in vitro (human & rat) • dose effect, time effect • Single and repetitive dose (in vivo) • Toxygates

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