Protein Interaction Networks Analysis and Prediction

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Lars Juhl Jensen

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

Protein–protein interaction networks Lars Juhl Jensen

Phase 1 association networks

who?

STRING

Jensen, Kuhn et al., Nucleic Acids Research , 2009

STITCH

Kuhn et al., Nucleic Acids Research , 2010

630 genomes

2.5 million proteins

~74,000 small molecules

genomic context

Korbel et al., Nature Biotechnology , 2004

Korbel et al., Nature Biotechnology , 2004

Korbel et al., Nature Biotechnology , 2004

gene coexpression

physical 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

confidence scores

benchmarking

von Mering et al., Nucleic Acids Research , 2005

transfer by orthology

protein mode

von Mering et al., Nucleic Acids Research , 2005

COG mode

von Mering et al., Nucleic Acids Research , 2005

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 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

Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

larsjuhljensen

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Protein Interaction Networks Analysis and Prediction

1. Protein–protein interaction networks Lars Juhl Jensen

2.

3.

4.

5.

6. Phase 1 association networks

8.

10. Jensen, Kuhn et al., Nucleic Acids Research , 2009

12. Kuhn et al., Nucleic Acids Research , 2010

13. 630 genomes

14. 2.5 million proteins

15. ~74,000 small molecules

16. genomic context

17. Korbel et al., Nature Biotechnology , 2004

18. Korbel et al., Nature Biotechnology , 2004

19. Korbel et al., Nature Biotechnology , 2004

20. gene coexpression

21.

22. physical interactions

23. Jensen & Bork, Science , 2008

24. genetic interactions

25. Beyer et al., Nature Reviews Genetics , 2007

26. curated knowledge

27. Letunic & Bork, Trends in Biochemical Sciences , 2008

28. literature mining

30.

31. confidence scores

32. benchmarking

33. von Mering et al., Nucleic Acids Research , 2005

34. transfer by orthology

35. protein mode

36. von Mering et al., Nucleic Acids Research , 2005

38. von Mering et al., Nucleic Acids Research , 2005

39. probabilistic integration

40. Frishman et al., Modern Genome Annotation , 2009

41. Phase 2 signaling networks

43. phosphoproteomics

44.

45. signaling events

46. sequence motifs

47. Miller, Jensen et al., Science Signaling , 2008

49. Miller, Jensen et al., Science Signaling , 2008

50.

52. Linding, Jensen, Ostheimer et al., Cell , 2007

53. benchmarking

54. Linding, Jensen, Ostheimer et al., Cell , 2007

55. context is crucial

57. DNA damage response

58. Linding, Jensen, Ostheimer et al., Cell , 2007

59. cell-cycle kinases

60. Olsen, Vermeulen et al., Science Signaling , 2010

61. Phase 3 dynamic networks

63. cell-cycle regulation

64.

65. microarray time courses

66. Gauthier et al., Nucleic Acids Research , 2007

67. protein interactions

68. temporal network

69. de Lichtenberg, Jensen et al., Science , 2005

70. de Lichtenberg, Jensen et al., Science , 2005

71. just-in-time assembly

72. de Lichtenberg, Jensen et al., Cell Cycle , 2007

73. evolutionary flexibility

74. individual genes

75. Jensen, Jensen, de Lichtenberg et al., Nature , 2006

76. protein complexes

77. Jensen, Jensen, de Lichtenberg et al., Nature , 2006

78. phosphorylation

79. co-evolution

80. Jensen, Jensen, de Lichtenberg et al., Nature , 2006

83. data integration

84. specific predictions

85. systems properties

86.

87.

88. larsjuhljensen

Notas do Editor

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