Data Integration & Systems Toxicology???Toxicogenomics is the study of the response of a genome to environmental stressors and toxicants.Combines genetics, genomic-scale mRNA expression (genomics), cell and tissue-wide protein expression (proteomics), metabolite profiling (metabolomics), and bioinformatics with conventional toxicology in an effort to understand the role of gene-environment interactions in disease.ToxicogenomicsCredit: M. Waters (NIEHS)-The Chemical Effects in Biological Systems (CEBS) knowledge base aims to be a dynamic system for integrating large volumes of disparate information in a framework that serves as a continually changing heuristic engine. - CEBS will evolve both in content and capabilities to become a “system of predictive toxicology.”-http://cebs.niehs.nih.gov/A Knowledge Base DefinedA knowledge base uses data and information to carry out tasks that create new information and new understanding.Credit: M. Waters (NIEHS)Systems Biology: a complete description of how the components of a biological system work togetherDescribe a systemMeasure changes globally Perturb a systemDevelop a better model of the systemIdeker, Galitski, & Hood (2001) A new approach to decoding life: systems biology. Ann Rev Genomics Hum Genet 2: 343-372.Waters and Fostel (2004) Toxicogenomics and systems toxicology: Aims and prospects. Nat Rev Genet 5: 936-948.Credit: M. Waters (NIEHS)Toxicogenomics ObjectivesCompare toxicogenomic effects of chemicals/ stressors across species- Yielding signatures of altered gene/protein expression“Phenotypically anchor” these changes with conventional toxicology data- Classifying effects as well as disease phenotypesDelineate global changes as adaptive, pharmacologic or toxic outcomes- Defining biomarkers, sequence of key events, mechanisms of actionWhy do we need Knowledge Bases?Credit: M. Waters (NIEHS)Contemporary Toxicology Experimental DesignMicroarrayAnalysisBioinformaticsanalysisIdentification ofcandidatebiomarkersVerifyToxicologicalCharacterization• acute toxicity• pathology• clinical chemistry• chronic toxicity• carcinogenicityFractionation of targetand non-target tissues2D-PAGE / MS SELDI Candidate proteinidentification (mass spec)Analysis of serum forcandidate proteinsBiomarker Discovery, Key events,Mechanisms of actionVerifyData IntegrationProteomic AnalysisChemical exposure of animal modelsCredit: M. Waters (NIEHS)?A Framework for Systems ToxicologyWaters & Fostel Nat Rev Genet (2004)Bioinformatics challenges and biological complexityWaters & Fostel Nat Rev Genet (2004)200 10000 50.00 5.644800 4800 1.00 0.009000 300 0.03 -4.91Cy3Cy5Cy5Cy3log2Cy5Cy3 Slide courtesy of C.M. PerouWhere does the data go?NAME BC/FUMI0 BC/FUMI4 BC/FUMI4 BC601B-ABC601A-BBC/FUMI1 BC/FUMI2 BC/FUMI2 BC/FUMI1 BC/FUMI1 BC102B-BBC/FUMI2 BC/FUMI3 BC/FUMI3 BC/FUMI1 BC/FUMI1adipose differentiation-related prote0.242 1.21 -0.253 -0.841 -0.423 -0.363 -0.852 -1.383 -2.642 0.501 -0.25 -0.605 -0.636 0.229 -0.626plasminogen activator, urokinase re0.908 0.485 -0.397 -0.767 -0.886 -0.251 -0.683 0.057 -0.317 -1.2 0.125 -0.536 -0.248 -0.365plasminogen activator, urokinase re0.4635 0.3545 -0.8975 -1.23 -0.8335 0.0175 -1.002 0.1555 -0.4325 -1.008 -0.1785 -0.7445 -0.1485 0.0555 0.2055coronin, actin binding protein, 1C A0.551 0.151 -0.422 0.007 -0.638 0.087 -0.689 -0.91 -0.853 0.052 -0.492 -0.201 -0.152 -0.368 -0.741**coatomer protein complex, subun-1.061 -0.8655 -0.1235 -0.9895 0.3815 -0.4955 -0.2775 -0.1465 -1.109 -0.8635 0.2615 -0.0905 -0.3225 -0.6035 0.0195 -0.9345coactosin-like protein R78490 -0.8835 -0.4545 0.2375 -1.177 0.2155 -0.2975 -0.9385 -0.2815 -1.494 -0.5985 0.4095 -0.3465 0.2185 -0.1345 -0.2895 -0.5525folylpolyglutamate synthase R448640.686 1.583 1.313 0.048 -0.272 -0.143 -0.394 0.423 -0.445 -0.854 0.322 -0.03 -0.412 0.214 -1.098 -0.175lysozyme (renal amyloidosis) N639-0.18 1.155 1.575 -1.635 0.355 0.295 -0.805 0.135 -2.145 -0.955 0.575 0.735 -0.435 -0.855 -0.8 -1.705chemokine (C-C motif) receptor 1 AA036881 0.524 1.233 -1.459 -0.095 -0.122 -0.196 0.101 -0.942 -0.2 -0.133 -0.549 -0.763 -0.059interferon, gamma-inducible protein-0.181 -0.062 0.37 0.064 0.418 -0.33 -0.098 -0.289 -1.042 -0.332 0.907 1.056 -0.8 -0.193 -0.789 -1.25cystatin B (stefin B) H22919 -0.188 -0.489 -0.603 0.074 -0.212 -0.295 -0.54 -0.535 -0.453 -0.479 -0.021 0.291 -0.651 -0.536 -0.401 -0.511cathepsin S AA236164 -0.791 0.334 -0.316 0.723 -0.46 0.39 -0.452 -0.413 1.063 -0.849 -1.088 -0.94 -1.291small inducible cytokine A2 (monoc0.2665 0.2955 0.5315 -0.1285 0.4255 -1.099 -0.7265 -0.6035 -1.052 -1.438 0.1355 0.0365 -0.4335 0.0875 -1.218 -0.7785natural killer cell transcript 4 AA4580.483 0.348 0.575 -0.685 0.971 -0.335 -0.222 -0.116 -1.644 -0.66 -0.322 0.885 -0.08 -0.02 -0.441 -0.51superoxide dismutase 2, mitochond0.431 0.301 -0.836 0.519 -0.492 -0.834 -0.86 0.781 0.005 -1.163 -1.283 -0.969 -0.586superoxide dismutase 2, mitochondrial AA48770.3185 -0.6835 0.4865 0.6925 -0.7895 -0.6005 -0.5815 0.4995 0.0165 0.3755 -0.1225 -1.129 -1.137 -0.6935transforming growth factor, beta-ind0.0235 0.6525 -0.3785 -0.5505 -0.3675 -0.4755 -0.1105 0.3435 0.0785 -0.4735 0.7925 1.532 -0.3355 -0.0885 0.2495 -0.1985glycine dehydrogenase (decarboxy-1.122 -1.412 -1.275 -1.764 -0.611 1.259 -1.25 -0.76 -2.159 -1.72 -1.017 -0.972 -0.715 -0.543 -0.658 -0.818syndecan 2 (heparan sulfate proteo-1.828 -1.7 -1.409 -1.964 -0.975 1.516 -1.24 -1.75 -2.219 -2.477 -1.08 0.29 -1.641 -2.045 -0.315 -1.356glutathione S-transferase pi R33642-1.726 -1.892 -1.568 1.528 -1.346 -2.157 -3.114 -3.146 -0.943 0.236 -1.349 -1.674 -0.416 -1.557chitinase 3-like 2 AA668821 -0.771 -1.436 -1.454 -0.813 -1.578 0.312 -0.167 0 -0.469 0.129 -0.566 -0.489nuclear factor I/B W87528 0.464 -1.314 -0.187 -1.429 -0.189 0.551 -1.94 -1.372 -2.152 -1.825 -0.441 -0.928 0.316 -1.188ras homolog gene family, member -1.382 -0.471 -0.421 0.304 -0.448 -0.805 -0.945 -0.737 -1.222 -0.915 -0.713 -0.167 0.09 1.074 -0.393ras homolog gene family, member -1.311 -0.763 -0.61 0.198 -0.764 -0.391 -0.867 -1.469 -1.106 -0.486 -0.778 -0.579 0.812 0.348 -0.222**zinc finger, DHHC domain containing 5 AA4-0.965 -0.571 -0.304 -0.328 -0.417 -0.518 -0.473 -0.973 -0.94 -0.926 -1.153 -0.462 -0.683 0.828 0.347keratin 5 (epidermolysis bullosa sim-0.309 -0.485 -0.748 -0.909 -0.403 -0.127 -0.371 -0.778 -1.596 -1.787 -0.782 0.242 -0.559 -0.804 0.79 0.374keratin 5 (epidermolysis bullosa simplex, Dowl -0.655 -2.421 0.301 0.689 -0.38 -0.131
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