systems biology biological sequence analysis 27803
Post on 19-Dec-2015
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TRANSCRIPT
Meet Your Instructor
• Christopher Workman– CBS-DTU– Regulatory Genomic– Integrative Systems Biology
Schedule for the morning
09:00 – 09:25 Pre-module quiz
09:25 – 09:50 Introduction and Motivation
09:50 – 10:20 Coffee Break
10:20 – 10:50 Interaction networks: data and properties
10:50 – 11:10 Discussion: Pluses/minuses of HTP interaction data sets
11:10 – 12:00 Exercise
“Genome scale” metabolic models
• Genes 708• Metabolites 584
– Cytosolic 559– Mitochondrial 164– Extracellular 121
• Reactions 1175– Cytosolic 702– Mitochondrial 124– Exchange fluxes 349
Forster et al. Genome Research 2003.
One framework for Systems Biology
1. The components. Discover all of the genes in the genome and the subset of genes, proteins, and other small molecules constituting the pathway of interest. If possible, define an initial model of the molecular interactions governing pathway function (how?).
2. Pathway perturbation. Perturb each pathway component through a series of genetic or environmental manipulations. Detect and quantify the corresponding global cellular response to each perturbation.
One framework for Systems Biology
3. Model Reconciliation. Integrate the observed mRNA and protein responses with the current, pathway-specific model and with the global network of protein-protein, protein-DNA, and other known physical interactions.
4. Model verification/expansion. Formulate new hypotheses to explain observations not predicted by the model. Design additional perturbation experiments to test these and iteratively repeat steps (2), (3), and (4).