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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 <ul><li>NetPhorest.info </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Martin Lee Miller </...
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Protein networks: A basis for large-scale data mining

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

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Protein networks: A basis for large-scale data mining

  1. 1. Protein networks A basis for large-scale data mining Lars Juhl Jensen
  2. 6. Phase 1 association networks
  3. 7. who?
  4. 9. STRING
  5. 10. Jensen, Kuhn et al., Nucleic Acids Research , 2009
  6. 11. genomic context
  7. 12. Korbel et al., Nature Biotechnology , 2004
  8. 13. gene coexpression
  9. 15. protein interactions
  10. 16. Jensen & Bork, Science , 2008
  11. 17. curated knowledge
  12. 18. Letunic & Bork, Trends in Biochemical Sciences , 2008
  13. 19. literature mining
  14. 21. confidence scores
  15. 22. von Mering et al., Nucleic Acids Research , 2005
  16. 23. transfer by orthology
  17. 24. probabilistic integration
  18. 25. Frishman et al., Modern Genome Annotation , 2009
  19. 26. Phase 2 signaling networks
  20. 27. what?
  21. 28. phosphoproteomics
  22. 30. signaling events
  23. 31. sequence motifs
  24. 32. Miller, Jensen et al., Science Signaling , 2008
  25. 33. NetPhorest
  26. 34. Miller, Jensen et al., Science Signaling , 2008
  27. 36. NetworKIN
  28. 37. Linding, Jensen, Ostheimer et al., Cell , 2007
  29. 38. benchmarking
  30. 39. Linding, Jensen, Ostheimer et al., Cell , 2007
  31. 40. context is crucial
  32. 41. use cases
  33. 42. DNA damage response
  34. 43. Linding, Jensen, Ostheimer et al., Cell , 2007
  35. 44. cell-cycle kinases
  36. 46. Phase 3 dynamic networks
  37. 47. when?
  38. 48. cell-cycle regulation
  39. 50. microarray time courses
  40. 51. Gauthier et al., Nucleic Acids Research , 2007
  41. 52. protein interactions
  42. 53. temporal network
  43. 54. de Lichtenberg, Jensen et al., Science , 2005
  44. 55. de Lichtenberg, Jensen et al., Science , 2005
  45. 56. just-in-time assembly
  46. 57. de Lichtenberg, Jensen et al., Cell Cycle , 2007
  47. 58. evolutionary flexibility
  48. 59. individual genes
  49. 60. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  50. 61. protein complexes
  51. 62. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  52. 63. phosphorylation
  53. 64. co-evolution
  54. 65. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
  55. 66. summary
  56. 67. networks
  57. 68. data integration
  58. 69. specific predictions
  59. 70. systems properties
  60. 72. Acknowledgments <ul><li>NetPhorest.info </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Martin Lee Miller </li></ul></ul><ul><ul><li>Francesca Diella </li></ul></ul><ul><ul><li>Claus Jørgensen </li></ul></ul><ul><ul><li>Michele Tinti </li></ul></ul><ul><ul><li>Lei Li </li></ul></ul><ul><ul><li>Marilyn Hsiung </li></ul></ul><ul><ul><li>Sirlester A. Parker </li></ul></ul><ul><ul><li>Jennifer Bordeaux </li></ul></ul><ul><ul><li>Thomas Sicheritz-Pontén </li></ul></ul><ul><ul><li>Marina Olhovsky </li></ul></ul><ul><ul><li>Adrian Pasculescu </li></ul></ul><ul><ul><li>Jes Alexander </li></ul></ul><ul><ul><li>Stefan Knapp </li></ul></ul><ul><ul><li>Nikolaj Blom </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Shawn Li </li></ul></ul><ul><ul><li>Gianni Cesareni </li></ul></ul><ul><ul><li>Tony Pawson </li></ul></ul><ul><ul><li>Benjamin E. Turk </li></ul></ul><ul><ul><li>Michael B. Yaffe </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><li>STRING-DB.org </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Chris Creevey </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Alexander Roth </li></ul></ul><ul><ul><li>Milan Simonovic </li></ul></ul><ul><ul><li>Jan Korbel </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Cyclebase.org </li></ul><ul><ul><li>Ulrik de Lichtenberg </li></ul></ul><ul><ul><li>Thomas Skøt Jensen </li></ul></ul><ul><ul><li>Nicholas Paul Gauthier </li></ul></ul><ul><ul><li>Rasmus Wernersson </li></ul></ul><ul><ul><li>Søren Brunak </li></ul></ul><ul><li>NetworKIN.info </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Gerard Ostheimer </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Martin Lee Miller </li></ul></ul><ul><ul><li>Francesca Diella </li></ul></ul><ul><ul><li>Karen Colwill </li></ul></ul><ul><ul><li>Jing Jin </li></ul></ul><ul><ul><li>Pavel Metalnikov </li></ul></ul><ul><ul><li>Vivian Nguyen </li></ul></ul><ul><ul><li>Adrian Pasculescu </li></ul></ul><ul><ul><li>Jin Gyoon Park </li></ul></ul><ul><ul><li>Leona D. Samson </li></ul></ul><ul><ul><li>Rob Russell </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Michael Yaffe </li></ul></ul><ul><ul><li>Tony Pawson </li></ul></ul>
  61. 73. larsjuhljensen

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