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Protein networks: A basis for large-scale data mining

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  • Integration Automation Collaboration
  • Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome

Protein networks: A basis for large-scale data mining Protein networks: A basis for large-scale data mining Presentation Transcript

  • Protein networks A basis for large-scale data mining Lars Juhl Jensen
  •  
  •  
  •  
  •  
  • Phase 1 association networks
  • who?
  •  
  • STRING
  • Jensen, Kuhn et al., Nucleic Acids Research , 2009
  • genomic context
  • Korbel et al., Nature Biotechnology , 2004
  • gene coexpression
  •  
  • protein interactions
  • Jensen & Bork, Science , 2008
  • curated knowledge
  • Letunic & Bork, Trends in Biochemical Sciences , 2008
  • literature mining
  • Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  • confidence scores
  • von Mering et al., Nucleic Acids Research , 2005
  • transfer by orthology
  • probabilistic integration
  • Frishman et al., Modern Genome Annotation , 2009
  • Phase 2 signaling networks
  • what?
  • phosphoproteomics
  •  
  • signaling events
  • sequence motifs
  • Miller, Jensen et al., Science Signaling , 2008
  • NetPhorest
  • Miller, Jensen et al., Science Signaling , 2008
  •  
  • NetworKIN
  • Linding, Jensen, Ostheimer et al., Cell , 2007
  • benchmarking
  • Linding, Jensen, Ostheimer et al., Cell , 2007
  • context is crucial
  • use cases
  • DNA damage response
  • Linding, Jensen, Ostheimer et al., Cell , 2007
  • cell-cycle kinases
  • Olsen, Vermeulen, Santamaria, Kumar et al., Science Signaling , 2010
  • Phase 3 dynamic networks
  • when?
  • cell-cycle regulation
  •  
  • microarray time courses
  • Gauthier et al., Nucleic Acids Research , 2007
  • protein interactions
  • temporal network
  • de Lichtenberg, Jensen et al., Science , 2005
  • de Lichtenberg, Jensen et al., Science , 2005
  • just-in-time assembly
  • de Lichtenberg, Jensen et al., Cell Cycle , 2007
  • evolutionary flexibility
  • individual genes
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • protein complexes
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • phosphorylation
  • co-evolution
  • Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  • summary
  • networks
  • data integration
  • specific predictions
  • systems properties
  •  
  • thank you!
  • Acknowledgments
    • NetPhorest.info
      • Rune Linding
      • Martin Lee Miller
      • Francesca Diella
      • Claus Jørgensen
      • Michele Tinti
      • Lei Li
      • Marilyn Hsiung
      • Sirlester A. Parker
      • Jennifer Bordeaux
      • Thomas Sicheritz-Pontén
      • Marina Olhovsky
      • Adrian Pasculescu
      • Jes Alexander
      • Stefan Knapp
      • Nikolaj Blom
      • Peer Bork
      • Shawn Li
      • Gianni Cesareni
      • Tony Pawson
      • Benjamin E. Turk
      • Michael B. Yaffe
      • Søren Brunak
    • STRING-DB.org
      • Christian von Mering
      • Damian Szklarczyk
      • Michael Kuhn
      • Manuel Stark
      • Samuel Chaffron
      • Chris Creevey
      • Jean Muller
      • Tobias Doerks
      • Philippe Julien
      • Alexander Roth
      • Milan Simonovic
      • Jan Korbel
      • Berend Snel
      • Martijn Huynen
      • Peer Bork
    • Cyclebase.org
      • Ulrik de Lichtenberg
      • Thomas Skøt Jensen
      • Nicholas Paul Gauthier
      • Rasmus Wernersson
      • Søren Brunak
    • NetworKIN.info
      • Rune Linding
      • Heiko Horn
      • Gerard Ostheimer
      • Martin Lee Miller
      • Francesca Diella
      • Karen Colwill
      • Jing Jin
      • Pavel Metalnikov
      • Vivian Nguyen
      • Adrian Pasculescu
      • Jin Gyoon Park
      • Leona D. Samson
      • Rob Russell
      • Peer Bork
      • Michael Yaffe
      • Tony Pawson
  • larsjuhljensen