Data Integration and Systems Biology

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Lars Juhl Jensen

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

Technologie

Lars Juhl Jensen Data Integration and Systems Biology

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

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

Miller, Jensen et al., Science Signaling , 2008

Jensen et al., Nucleic Acids Research , 2008

Korbel et al., Nature Biotechnology , 2004

Letunic & Bork, Trends in Biochemical Sciences , 2008

von Mering et al., Nucleic Acids Research , 2005

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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

5. a good idea

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

21. in vivo

22. kinases are unknown

23. peptide assays

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

25. sequence specificity

26. kinase-specific

27. in vitro

28. no context

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

35. no context

36. what a kinase could do

37. not what it actually does

38. in vitro

39. in vivo

40. context

41. co-activators

42. scaffolders

43. expression

44. association networks

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

46. the idea

47. mass spectrometry

48. phosphorylation sites

49. sequence motifs

50. sequence specificity

51. association network

52. context

53. in vitro

54. in vivo

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

56. the sequence motifs

57. NetPhorest

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

59. pipeline

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

77. WW 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

87. STRING

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

108. parsers

109. different gene identifiers

110. thesaurus

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

122. NetworKIN

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