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Protein networks: A basis for large-scale data mining

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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. 2. Phase 1 association networks
  3. 3. who?
  4. 4. STRING
  5. 5. Jensen, Kuhn et al., Nucleic Acids Research, 2009
  6. 6. genomic context
  7. 7. Korbel et al., Nature Biotechnology, 2004
  8. 8. gene coexpression
  9. 9. protein interactions
  10. 10. Jensen & Bork, Science, 2008
  11. 11. curated knowledge
  12. 12. Letunic & Bork, Trends in Biochemical Sciences, 2008
  13. 13. literature mining
  14. 14. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
  15. 15. confidence scores
  16. 16. von Mering et al., Nucleic Acids Research, 2005
  17. 17. transfer by orthology
  18. 18. probabilistic integration
  19. 19. Frishman et al., Modern Genome Annotation, 2009
  20. 20. Phase 2 signaling networks
  21. 21. what?
  22. 22. phosphoproteomics
  23. 23. signaling events
  24. 24. sequence motifs
  25. 25. Miller, Jensen et al., Science Signaling, 2008
  26. 26. NetPhorest
  27. 27. Miller, Jensen et al., Science Signaling, 2008
  28. 28. NetworKIN
  29. 29. Linding, Jensen, Ostheimer et al., Cell, 2007
  30. 30. benchmarking
  31. 31. Linding, Jensen, Ostheimer et al., Cell, 2007
  32. 32. context is crucial
  33. 33. use cases
  34. 34. DNA damage response
  35. 35. Linding, Jensen, Ostheimer et al., Cell, 2007
  36. 36. cell-cycle kinases
  37. 37. Olsen, Vermeulen, Santamaria, Kumar et al., Science Signaling, 2010
  38. 38. Phase 3 dynamic networks
  39. 39. when?
  40. 40. cell-cycle regulation
  41. 41. microarray time courses
  42. 42. Gauthier et al., Nucleic Acids Research, 2007
  43. 43. protein interactions
  44. 44. temporal network
  45. 45. de Lichtenberg, Jensen et al., Science, 2005
  46. 46. de Lichtenberg, Jensen et al., Science, 2005
  47. 47. just-in-time assembly
  48. 48. de Lichtenberg, Jensen et al., Cell Cycle, 2007
  49. 49. evolutionary flexibility
  50. 50. individual genes
  51. 51. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
  52. 52. protein complexes
  53. 53. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
  54. 54. phosphorylation
  55. 55. co-evolution
  56. 56. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
  57. 57. summary
  58. 58. networks
  59. 59. data integration
  60. 60. specific predictions
  61. 61. systems properties
  62. 62. thank you!
  63. 63. 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
  64. 64. larsjuhljensen

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