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Protein networks: A basis for large-scale data mining

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Lars Juhl Jensen
Lars Juhl Jensen
Technology
1 of 74
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

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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