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Mining heterogeneous data: Understanding systems at the level of complexes and networks
 

Mining heterogeneous data: Understanding systems at the level of complexes and networks

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    Mining heterogeneous data: Understanding systems at the level of complexes and networks Mining heterogeneous data: Understanding systems at the level of complexes and networks Presentation Transcript

    • Mining heterogeneous data Understanding systems at the level of complexes and networks Lars Juhl Jensen
    • the cell cycle
    • grow and divide
    • one cell
    • two cells
    • four phases
    • G 1 phase
    • growth
    • S phase
    • DNA replication
    • G 2 phase
    • growth
    • M phase
    • cell division
    •  
    • regulation
    • gene expression
    • protein complexes
    • phosphorylation
    • targeted degradation
    • gene expression
    • cell cultures
    • S. cerevisiae
    •  
    • synchronization
    • microarrays
    •  
    • time courses
    • Gauthier et al., Nucleic Acids Research , 2007
    • cycling genes
    • scoring scheme
    • shape
    • magnitude
    • benchmarking
    • Gauthier et al., Nucleic Acids Research , 2007
    • protein complexes
    • interaction data
    • S. cerevisiae
    • Jensen & Bork, Science , 2008
    •  
    • high error rate
    • scoring scheme
    • von Mering et al., Nucleic Acids Research , 2005
    • calibrate against KEGG
    •  
    • quality threshold
    • temporal network
    • time of peak mRNA level
    • time of protein synthesis
    • de Lichtenberg, Jensen et al., Science , 2005
    • de Lichtenberg, Jensen et al., Science , 2005
    • hypothesis
    • just-in-time assembly
    • de Lichtenberg, Jensen et al., Cell Cycle , 2007
    • how can we test it?
    • evolution
    • microarray time courses
    • S. pombe
    • H. sapiens
    • A. thaliana
    • reanalysis
    • cycling genes
    • same algorithm
    • cross-species comparison
    • orthologous genes
    • sequence similarity
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • protein complexes
    • DNA polymerases
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • all cell-cycle complexes
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • time of peak mRNA level
    • time of action
    • just-in-time assembly
    • generalize to metabolism
    • linear pathways
    • deoxynucleotide synthesis
    •  
    • just-in-time flux
    • cell-cycle phenotypes
    • H. sapiens
    • siRNA screen
    • comparison with expression
    •  
    • phosphorylation
    •  
    • CDK substrate
    • low-throughput data
    • high-throughput data
    • NetPhosK
    • correlation
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • bias
    • correlated changes
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    • co-evolution
    • layers of regulation
    • summary
    • reanalysis
    • integration
    • high-throughput data
    • biological insights
    • Acknowledgments
      • Thomas Skøt Jensen
      • Ulrik de Lichtenberg
      • Søren Brunak
      • Peer Bork
    • larsjuhljensen
    •