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
gene fusion
Korbel et al., Nature Biotechnology, 2004
conserved neighborhood
Korbel et al., Nature Biotechnology, 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology, 2004
gene coexpression
protein interactions
Jensen & Bork, Science, 2008
genetic interactions
Beyer et al., Nature Reviews Genetics, 2007
curated knowledge
Letunic & Bork, Trends in Biochemical Sciences, 2008
literature mining
>10 km
co-mentioning
NLP
Natural Language Processing
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. gene fusion
    8. 8. Korbel et al., Nature Biotechnology, 2004
    9. 9. conserved neighborhood
    10. 10. Korbel et al., Nature Biotechnology, 2004
    11. 11. phylogenetic profiles
    12. 12. Korbel et al., Nature Biotechnology, 2004
    13. 13. gene coexpression
    14. 14. protein interactions
    15. 15. Jensen & Bork, Science, 2008
    16. 16. genetic interactions
    17. 17. Beyer et al., Nature Reviews Genetics, 2007
    18. 18. curated knowledge
    19. 19. Letunic & Bork, Trends in Biochemical Sciences, 2008
    20. 20. literature mining
    21. 21. >10 km
    22. 22. co-mentioning
    23. 23. NLP Natural Language Processing
    24. 24. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
    25. 25. confidence scores
    26. 26. von Mering et al., Nucleic Acids Research, 2005
    27. 27. transfer by orthology
    28. 28. probabilistic integration
    29. 29. Frishman et al., Modern Genome Annotation, 2009
    30. 30. Phase 2 signaling networks
    31. 31. what?
    32. 32. phosphoproteomics
    33. 33. signaling events
    34. 34. sequence motifs
    35. 35. Miller, Jensen et al., Science Signaling, 2008
    36. 36. NetPhorest
    37. 37. Miller, Jensen et al., Science Signaling, 2008
    38. 38. NetworKIN
    39. 39. Linding, Jensen, Ostheimer et al., Cell, 2007
    40. 40. benchmarking
    41. 41. Linding, Jensen, Ostheimer et al., Cell, 2007
    42. 42. context is crucial
    43. 43. use cases
    44. 44. DNA damage response
    45. 45. Linding, Jensen, Ostheimer et al., Cell, 2007
    46. 46. cell-cycle kinases
    47. 47. Olsen, Vermeulen, Santamaria, Kumar et al., Science Signaling, 2010
    48. 48. Phase 3 dynamic networks
    49. 49. when?
    50. 50. cell-cycle regulation
    51. 51. microarray time courses
    52. 52. Gauthier et al., Nucleic Acids Research, 2007
    53. 53. protein interactions
    54. 54. temporal network
    55. 55. de Lichtenberg, Jensen et al., Science, 2005
    56. 56. de Lichtenberg, Jensen et al., Science, 2005
    57. 57. just-in-time assembly
    58. 58. de Lichtenberg, Jensen et al., Cell Cycle, 2007
    59. 59. evolutionary flexibility
    60. 60. individual genes
    61. 61. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
    62. 62. protein complexes
    63. 63. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
    64. 64. phosphorylation
    65. 65. co-evolution
    66. 66. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
    67. 67. summary
    68. 68. networks
    69. 69. data integration
    70. 70. specific predictions
    71. 71. systems properties
    72. 72. thank you!
    73. 73. 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
    74. 74. larsjuhljensen
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