bioinformatics and toxicology - university of birmingham · 2020. 6. 13. · what is...
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Bioinformatics and Toxicology
Philipp Antczak
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What is Bioinformatics?
• It is the application of statistics and computer science to the field of molecular biology and medicine.
– Analysis of Cancer mutations
– Analysis of Gene Expression
– DNA Sequence Analysis
– Simulations and Modelling
– etc
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Tools
• Sequence Analysis Tools – DNA sequence analysis
• Image Processing – Microarray image analysis
• Exploratory Algorithms – Principle Component Analysis (PCA) – Hierarchical clustering
• Statistical Tests – Identify differentially expressed features – Classification algorithms – Modelling
• Networks – Building large networks based on high density data – Identifying sub-networks which may be indicative of
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Case Study – Applying Bioinformatics to a problem in Toxicology
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Daphnia Magna
• Wide Geographic Distribution
• Central role in freshwater food webs
• Ability to adapt to a range of habitats
• Highly sensitive to anthropogenic chemicals
• Analysed their gene expression using microarrays
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The aims of this project
• Identify whether similar chemicals (such as metals or a specific subgroup) act similarly on an organism
• Is it possible to apply methodologies developed in biomedical research to toxicology?
• Identify whether Daphnia magna can be used to sense specific chemicals in a sample
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The Dataset
• Dataset was provided by Chris Vulpe laboratory at the University of California, Berkley
• 14 day adult D. magna
– Exposed these to the 36 chemicals at 1/10 of measured LD50
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Data
Can we predict chemical class from gene expression
profiles?
Can we predict measured Toxicity (LD50)?
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Exploratory Analysis
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PCA of Dataset
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Benzene Endocrine Herbicide Industrial Metals Organophosphates Pyrethroids
Hierarchical Clustering of Differentially Expressed Genes
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Classification
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How well can I predict a chemical group?
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Regression Modelling
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gfedcbaLD i 32312132150
Can we predict Toxicity?
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Other Applications
• Water quality assessment – Predicting what is in the water we drink using for
example Daphnia Magna
• Drug Development – Will a new drug be effective?
• Biomedical research – Develop drugs specific for human diseases
– Provide the population with better foods, i.e. less pesticides or other toxins
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Acknowledgments
University of Birmingham Dr. Francesco Falciani – Systems Biology Nil Turan Kim Clarke Wazeer Varsally Rita Gupta Jaanika Kronberg Helani Munasinghe Prof. Mark Viant– local Daphnia Experts Thomas White
University of California, Berkeley Prof. Chris Vulpe – U.S. Partners, data acquisition Leona Scandlan
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