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Protein networks: A basis for large-scale data mining

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Lars Juhl Jensen
Lars Juhl Jensen

4th Novo Nordisk TRAP Symposium, Novo Nordisk, Bagsværd, Denmark, October 27, 2009.

Technology
1 of 73
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
 
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
 
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
 
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
larsjuhljensen

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Protein networks: A basis for large-scale data mining

Editor's Notes

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