c06_netw_prop_bio

c06_netw_prop_bio - The The structure of molecular cellular...

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The structure of molecular & cellular etworks networks To be able to construct and analyze a cellular network, we need to clearly define what we identify as a node and what we represent with an edge. The nodes and edges have to be at least similar to each other, g represent the same type of cellular component (protein e.g. represent the same type of cellular component (protein, chemical) or the same type of interaction (mass transfer, regulation). We can, and often need to, define different types of nodes and edges.
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Life at the cellular level • Cellular functions rely on the ordinated action of interacting coordinated action of interacting components. roteins Proteins – provide structure to cells and tissues – work as molecular motors nse chemicals in the environment sense chemicals in the environment – drive chemical reactions – regulate gene expression • Interconnections between components are the essence fl i i avid Goodsell/ Science Photo Library receptor proteins , enzymes , ribosomes , DNA of a living process. David Goodsell/ Science Photo Library
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Frequently defined molecular interaction networks gene regulatory network protein-protein teraction interaction network external signals signal transduction network bio-chemical action Citrate Cycle reaction network
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Examples of intracellular networks 1. Protein interaction networks nodes: proteins edges: protein-protein interactions (binding), modification of a protein 2. Biochemical reaction networks odes: nodes: reactants (substrates) or products of the reactions enzymes – catalyze the reactions reactant-enzyme complex (“reaction node”) edges: reactions catalysis (regulation)
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Examples of intracellular networks (cont.) 3. Gene regulatory networks nodes: gene, mRNA, protein edges: transcription, translation, regulation 4. Signal transduction networks odes: nodes: proteins, molecules edges: reactions and processes (e.g. ligand-receptor interaction)
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Example of high-throughput experimental methods to map interactions ranscription factors bind to the Transcription factors bind to the promoter regions of genes. They have a DNA binding domain and an activation domain. In the two-hybrid method the two domains are separated, and fused to two proteins. If the two proteins interact by binding, the transcription factor activates the xpression of a reporter gene expression of a reporter gene. Systematic experiments with all roteins in a given organism lead to proteins in a given organism lead to genome-wide protein interaction maps.
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Mapping of cellular interaction networks Experimental advances allow the construction of genome-wide pg cellular interaction networks Protein networks: Individual studies: etz et al 2000 Ito et al 2001 Krogan et al 2006 Yu et al 2008 Uetz et al. 2000, Ito et al. 2001, Krogan et al. 2006, Yu et al. 2008 – S.
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This document was uploaded on 03/01/2011.

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c06_netw_prop_bio - The The structure of molecular cellular...

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