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
– ...
larsjuhljensen
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
Protein networks: A basis for large-scale data mining
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Protein networks: A basis for large-scale data mining

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