Data Integration and Systems Biology

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Lars Juhl Jensen

Danish Protein Science Meeting, Skt. Helene, Tisvildeleje, Denmark, November 6-7, 2008

Lars Juhl Jensen Data Integration and Systems Biology

Lars Juhl Jensen Data Integration and Systems Biology

what went wrong?

a good problem

a good idea

cell-cycle regulation

microarray data

interaction network

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

new uses for old drugs

chemical similarity

side effects

the problem

phosphorylation networks

mass spectrometry

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

phosphorylation sites

in vivo

kinases are unknown

peptide assays

Miller, Jensen et al., Science Signaling , 2008

sequence specificity

kinase-specific

in vitro

no context

what a kinase could do

not what it actually does

computational methods

sequence specificity

Miller, Jensen et al., Science Signaling , 2008

kinase-specific

no context

what a kinase could do

not what it actually does

in vitro

in vivo

context

co-activators

scaffolders

expression

association networks

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

the idea

mass spectrometry

phosphorylation sites

sequence motifs

sequence specificity

association network

context

in vitro

in vivo

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

the sequence motifs

NetPhorest

Miller, Jensen et al., Science Signaling , 2008

pipeline

data organization

Miller, Jensen et al., Science Signaling , 2008

compilation of datasets

Miller, Jensen et al., Science Signaling , 2008

redundancy reduction

Miller, Jensen et al., Science Signaling , 2008

cross-validation partitioning

Miller, Jensen et al., Science Signaling , 2008

training and evaluation

classifier selection

Miller, Jensen et al., Science Signaling , 2008

motif atlas

179 kinases

93 SH2 domains

8 PTB domains

BRCT domains

WW domains

14-3-3 proteins

benchmarking

Miller, Jensen et al., Science Signaling , 2008

low-specificity kinases

disease-related kinases

Miller, Jensen et al., Science Signaling , 2008

docking domains

Miller, Jensen et al., Science Signaling , 2008

the context network

STRING

functional associations

373 genomes

Jensen et al., Nucleic Acids Research , 2008

genomic context methods

gene fusion

Korbel et al., Nature Biotechnology , 2004

conserved neighborhood

Korbel et al., Nature Biotechnology , 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology , 2004

primary experimental data

protein interactions

Jensen & Bork, Science , 2008

gene coexpression

literature mining

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences , 2008

different formats

parsers

different gene identifiers

thesaurus

redundancy

bookkeeping

variable reliability

benchmarking

von Mering et al., Nucleic Acids Research , 2005

spread over many species

transfer by orthology

von Mering et al., Nucleic Acids Research , 2005

combine all evidence

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

the results

NetworKIN

123 kinases

5515 substrates

21,702 sites

benchmarking

Phospho.ELM

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

2.5-fold better accuracy

context is crucial

ATM signaling

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

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

small-scale validation

ATM phosphorylates Rad50

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

high-throughput validation

multiple reaction monitoring

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

systematic validation

kinase inhibitor matrix

Fedorov et al., PNAS , 2007

design optimal experiments

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http://larsjuhljensen.wordpress.com

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Data Integration and Systems Biology

1. Lars Juhl Jensen Data Integration and Systems Biology

2. Lars Juhl Jensen Data Integration and Systems Biology

3. what went wrong?

4. a good problem

6. cell-cycle regulation

7. microarray data

8. interaction network

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

10. new uses for old drugs

11. chemical similarity

12. side effects

13.

14.

15.

16. the problem

17. phosphorylation networks

18. mass spectrometry

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

20. phosphorylation sites

22. kinases are unknown

23. peptide assays

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

25. sequence specificity

26. kinase-specific

29. what a kinase could do

30. not what it actually does

31. computational methods

32. sequence specificity

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

34. kinase-specific

36. what a kinase could do

37. not what it actually does

41. co-activators

42. scaffolders

44. association networks

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

47. mass spectrometry

48. phosphorylation sites

49. sequence motifs

50. sequence specificity

51. association network

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

56. the sequence motifs

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

60. data organization

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

62. compilation of datasets

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

64. redundancy reduction

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

66. cross-validation partitioning

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

68. training and evaluation

69. classifier selection

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

71. motif atlas

72.

73. 179 kinases

74. 93 SH2 domains

75. 8 PTB domains

76. BRCT domains

78. 14-3-3 proteins

79. benchmarking

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

81. low-specificity kinases

82. disease-related kinases

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

84. docking domains

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

86. the context network

88. functional associations

89. 373 genomes

90. Jensen et al., Nucleic Acids Research , 2008

91. genomic context methods

92. gene fusion

93. Korbel et al., Nature Biotechnology , 2004

94. conserved neighborhood

95. Korbel et al., Nature Biotechnology , 2004

96. phylogenetic profiles

97. Korbel et al., Nature Biotechnology , 2004

98. primary experimental data

99. protein interactions

100. Jensen & Bork, Science , 2008

101. gene coexpression

102.

103. literature mining

104.

105. curated knowledge

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

107. different formats

109. different gene identifiers

111. redundancy

112. bookkeeping

113. variable reliability

114. benchmarking

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

116. spread over many species

117. transfer by orthology

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

119. combine all evidence

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

121. the results

123. 123 kinases

124. 5515 substrates

125. 21,702 sites

126. benchmarking

127. Phospho.ELM

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

129. 2.5-fold better accuracy

130. context is crucial

131. ATM signaling

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

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

134. small-scale validation

135. ATM phosphorylates Rad50

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

137. high-throughput validation

138. multiple reaction monitoring

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

140. systematic validation

141. kinase inhibitor matrix

142. Fedorov et al., PNAS , 2007

143. design optimal experiments

144.

145. http://larsjuhljensen.wordpress.com