Information integration

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Lars Juhl Jensen

Information integration

Lars Juhl Jensen

Part 1
the eukaryotic cell cycle

essential process

grow and divide

one cell

two cells

four phases

G1 phase

growth

S phase

DNA replication

G2 phase

growth

M phase

cell division

regulation

gene expression

phosphorylation

targeted degradation

protein interactions

Example 1
my protein and friends

http://string-db.org

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

Part 2
association networks

guild by association

STRING

>1100 genomes

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

protein interactions

Jensen & Bork, Science, 2008

genetic interactions

Beyer et al., Nature Reviews Genetics, 2007

gene coexpression

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences, 2008

>10 km

text mining

co-mentioning

NLP
Natural Language Processing

Gene and protein names
Cue words for entity recognition
Verbs for relation extraction

[nxgene The GAL4 gene]

[nxexpr The expression of
[nxgene the cytochrome genes
[nxpg CYC1 and CYC7]]]
is controlled by
[nxpg HAP1]

different sources

different formats

different names

not comparable

variable quality

many parsers

comprehensive lexicon

quality scores

look at the data

von Mering et al., Nucleic Acids Research, 2005

scoring scheme

benchmark

von Mering et al., Nucleic Acids Research, 2005

probabilistic scores

combine scores

Example 2
evidence filters and viewers

highest confidence only

experiments only

evidence viewers

Part 3
analysis of cell-cycle data

gene expression

cell cultures

synchronization

microarrays

time courses

look at the data

Gauthier et al., Nucleic Acids Research, 2007

scoring scheme

benchmark

time of peak expression

protein interactions

temporal network

de Lichtenberg, Jensen et al., Science, 2005

Example 3
a network for my proteins

http://string-db.org

high confidence only

experiments only

network expansion

Part 4
external data

save network

open in Cytoscape

layout

clustering

project data onto network

de Lichtenberg, Jensen et al., Science, 2005

very flexible

lose the STRING interface

payload mechanism

show external data

nodes

edges

hosted on your server

Example 4
my data in STRING

http://cyclebase-string.jensenlab.org

Conclusions

know your question

collect data

look at the data

benchmark

Thank you!

larsjuhljensen

Information integration

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Information integration

1. Information integration Lars Juhl Jensen

2.

3.

4.

5.

6. Part 1 the eukaryotic cell cycle

7. essential process

8. grow and divide

11. four phases

15. DNA replication

19. cell division

20.

22. gene expression

23. phosphorylation

24. targeted degradation

25. protein interactions

26. Example 1 my protein and friends

27. http://string-db.org

28. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

29.

30.

31. Part 2 association networks

32. guild by association

33.

35. >1100 genomes

36. genomic context

37. gene fusion

38. Korbel et al., Nature Biotechnology, 2004

39. conserved neighborhood

40. Korbel et al., Nature Biotechnology, 2004

41. phylogenetic profiles

42. Korbel et al., Nature Biotechnology, 2004

43. protein interactions

44. Jensen & Bork, Science, 2008

45. genetic interactions

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

47. gene coexpression

48.

49. curated knowledge

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

52. text mining

53. co-mentioning

54. NLP Natural Language Processing

55. Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxgene The GAL4 gene] [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]

56. different sources

57. different formats

58. different names

59. not comparable

60. variable quality

61. many parsers

62. comprehensive lexicon

63. quality scores

64. look at the data

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

66. scoring scheme

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

69. probabilistic scores

70. combine scores

71. Example 2 evidence filters and viewers

72.

73.

74. highest confidence only

75.

76. experiments only

77.

78. evidence viewers

79.

80.

81. Part 3 analysis of cell-cycle data

82. gene expression

83. cell cultures

84. synchronization

85. microarrays

86. time courses

87. look at the data

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

89. scoring scheme

91. time of peak expression

92.

93. protein interactions

94. temporal network

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

96. Example 3 a network for my proteins

97. http://string-db.org

98.

99.

100. high confidence only

101. experiments only

102.

103. network expansion

104.

105.

106. Part 4 external data

107. save network

108.

109. open in Cytoscape

111. clustering

112. project data onto network

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

114. very flexible

115. lose the STRING interface

116. payload mechanism

117. show external data

120. hosted on your server

121. Example 4 my data in STRING

122. http://cyclebase-string.jensenlab.org

123.

124.

125.

126. Conclusions

127. know your question

128. collect data

129. look at the data

131.

132. Thank you!

133. larsjuhljensen