Mining heterogeneous data: Understanding systems at the level of complexes and networks
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Transcript of Mining heterogeneous data: Understanding systems at the level of complexes and networks
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Mining heterogeneous dataUnderstanding systems at the level of complexes and networks
Lars Juhl Jensen
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the cell cycle
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grow and divide
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one cell
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two cells
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four phases
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G1 phase
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growth
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S phase
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DNA replication
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G2 phase
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growth
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M phase
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cell division
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regulation
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gene expression
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protein complexes
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phosphorylation
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targeted degradation
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gene expression
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cell cultures
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S. cerevisiae
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synchronization
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microarrays
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time courses
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Gauthier et al., Nucleic Acids Research, 2007
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cycling genes
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scoring scheme
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shape
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magnitude
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benchmarking
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Gauthier et al., Nucleic Acids Research, 2007
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protein complexes
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interaction data
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Jensen & Bork, Science, 2008
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high error rate
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scoring scheme
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von Mering et al., Nucleic Acids Research, 2005
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von Mering et al., Nucleic Acids Research, 2005
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quality threshold
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time of peak mRNA level
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temporal network
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de Lichtenberg, Jensen et al., Science, 2005
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hypothesis
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just-in-time assembly
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de Lichtenberg, Jensen et al., Cell Cycle, 2007
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how can we test it?
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evolution
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microarray time courses
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S. pombe
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H. sapiens
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A. thaliana
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cross-species comparison
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orthologous genes
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sequence similarity
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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protein complexes
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all cell-cycle complexes
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Jensen, Jensen, de Lichtenberg et al., Nature, 2006
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time of peak mRNA level
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time of action
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just-in-time assembly
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pathways
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generalize to metabolism
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deoxynucleotide synthesis
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just-in-time flux
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phenotypes
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H. sapiens
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siRNA screen
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comparison with expression
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summary
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reanalysis
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integration
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high-throughput data
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biological insights
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Acknowledgments
Thomas Skøt JensenUlrik de Lichtenberg
Søren BrunakPeer Bork
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larsjuhljensen