Protein–protein interaction networks

1,378 views

Published on

Exploring Modular Protein Architecture, European Molecular Biology Laboratory, Heidelberg, Germany, January 19-22, 2010.

0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
1,378
On SlideShare
0
From Embeds
0
Number of Embeds
5
Actions
Shares
0
Downloads
69
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide
  • Integration Automation Collaboration
  • Atlas of human kinases Atlases for phospho-binding proteins Atlases for model organisms Ubiquitination would be welcome
  • Protein–protein interaction networks

    1. 1. Protein–protein interaction networks 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. STITCH
    7. 12. Kuhn et al., Nucleic Acids Research , 2010
    8. 13. 630 genomes
    9. 14. 2.5 million proteins
    10. 15. ~74,000 small molecules
    11. 16. genomic context
    12. 17. Korbel et al., Nature Biotechnology , 2004
    13. 18. Korbel et al., Nature Biotechnology , 2004
    14. 19. Korbel et al., Nature Biotechnology , 2004
    15. 20. gene coexpression
    16. 22. physical interactions
    17. 23. Jensen & Bork, Science , 2008
    18. 24. genetic interactions
    19. 25. Beyer et al., Nature Reviews Genetics , 2007
    20. 26. curated knowledge
    21. 27. Letunic & Bork, Trends in Biochemical Sciences , 2008
    22. 28. literature mining
    23. 29. >10 km
    24. 31. confidence scores
    25. 32. benchmarking
    26. 33. von Mering et al., Nucleic Acids Research , 2005
    27. 34. transfer by orthology
    28. 35. protein mode
    29. 36. von Mering et al., Nucleic Acids Research , 2005
    30. 37. COG mode
    31. 38. von Mering et al., Nucleic Acids Research , 2005
    32. 39. probabilistic integration
    33. 40. Frishman et al., Modern Genome Annotation , 2009
    34. 41. Phase 2 signaling networks
    35. 42. what?
    36. 43. phosphoproteomics
    37. 45. signaling events
    38. 46. sequence motifs
    39. 47. Miller, Jensen et al., Science Signaling , 2008
    40. 48. NetPhorest
    41. 49. Miller, Jensen et al., Science Signaling , 2008
    42. 51. NetworKIN
    43. 52. Linding, Jensen, Ostheimer et al., Cell , 2007
    44. 53. benchmarking
    45. 54. Linding, Jensen, Ostheimer et al., Cell , 2007
    46. 55. context is crucial
    47. 56. use cases
    48. 57. DNA damage response
    49. 58. Linding, Jensen, Ostheimer et al., Cell , 2007
    50. 59. cell-cycle kinases
    51. 60. Olsen, Vermeulen et al., Science Signaling , 2010
    52. 61. Phase 3 dynamic networks
    53. 62. when?
    54. 63. cell-cycle regulation
    55. 65. microarray time courses
    56. 66. Gauthier et al., Nucleic Acids Research , 2007
    57. 67. protein interactions
    58. 68. temporal network
    59. 69. de Lichtenberg, Jensen et al., Science , 2005
    60. 70. de Lichtenberg, Jensen et al., Science , 2005
    61. 71. just-in-time assembly
    62. 72. de Lichtenberg, Jensen et al., Cell Cycle , 2007
    63. 73. evolutionary flexibility
    64. 74. individual genes
    65. 75. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    66. 76. protein complexes
    67. 77. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    68. 78. phosphorylation
    69. 79. co-evolution
    70. 80. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
    71. 81. summary
    72. 82. networks
    73. 83. data integration
    74. 84. specific predictions
    75. 85. systems properties
    76. 87. 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>
    77. 88. larsjuhljensen

    ×