Just-in-time assembly Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes La...
the cell cycle
grow and divide
one cell
two cells
four phases
G 1  phase
growth
S phase
DNA replication
G 2  phase
growth
M phase
cell division
 
regulation
gene expression
phosphorylation
targeted degradation
protein interactions
molecular biology
one gene
one postdoc
many types of data
a single gene
high-throughput biology
one lab
one technology
all the relevant genes
a single type of data
systems biology
many types of data
all the relevant genes
data integration
expression data
cell cultures
 
synchronization
microarrays
 
time courses
 
expression profiles
 
list of genes
periodically expressed
S. cerevisiae
expression data
Cho et al.
Spellman et al.
computational methods
Zhao et al.
Langmead et al.
Johansson et al.
Wichert et al.
Luan and Li
Lu et al.
Ahdesm äki et al.
Willbrand et al.
Chen
Qiu et al.
Ahnert et al.
Glynn et al.
Andersson et al.
Lu et al.
Xu et al.
Liew et al.
no benchmarking
reanalysis
benchmarking
 
no progress
no benchmarking
S. pombe
H. sapiens
A. thaliana
reanalysis
benchmarking
list of genes
periodically expressed
four organisms
orthologous groups
sequence similarity
 
not conserved
others had seen the same
Ota et al.
Rustici et al.
Dyczkowski and Vingron
no explanation
a long time ago in a journal far, far away …
(Science, 2005)
temporal network
 
dynamic and static subunits
just-in-time assembly
 
evolutionary flexibility
different organisms
different dynamic subunits
manual curation
protein complexes
 
 
 
different time scales
time warping
same color = same phase
deoxynucleotide synthesis
 
dynamic subunits
time of peak expression
time of action
just-in-time assembly
 
CDK substrates
Phospho.ELM
Übersax et al.
Loog et al.
NetPhosK
correlation
 
Fisher’s exact test
 
cell cycle vs. non-cell cycle
correlated changes
 
Fisher’s exact test
 
co-evolution
transcriptional regulation
phosphorylation
targeted degradation
just-in-time assembly
 
summary
reanalysis
benchmarking
integration
high-throughput data
reproduce what is know
biological discoveries
testable hypotheses
protein complex regulation
evolution
Acknowledgments <ul><li>Thomas Skøt Jensen </li></ul><ul><li>Ulrik de Lichtenberg </li></ul><ul><li>Søren Brunak </li></ul...
Thank you!
Questions?
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Just-in-time assembly - Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes

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European Bioinformatics Institute, Hinxton, England, May 21, 2007

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Just-in-time assembly - Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes

  1. 1. Just-in-time assembly Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes Lars Juhl Jensen EMBL Heidelberg
  2. 2. the cell cycle
  3. 3. grow and divide
  4. 4. one cell
  5. 5. two cells
  6. 6. four phases
  7. 7. G 1 phase
  8. 8. growth
  9. 9. S phase
  10. 10. DNA replication
  11. 11. G 2 phase
  12. 12. growth
  13. 13. M phase
  14. 14. cell division
  15. 16. regulation
  16. 17. gene expression
  17. 18. phosphorylation
  18. 19. targeted degradation
  19. 20. protein interactions
  20. 21. molecular biology
  21. 22. one gene
  22. 23. one postdoc
  23. 24. many types of data
  24. 25. a single gene
  25. 26. high-throughput biology
  26. 27. one lab
  27. 28. one technology
  28. 29. all the relevant genes
  29. 30. a single type of data
  30. 31. systems biology
  31. 32. many types of data
  32. 33. all the relevant genes
  33. 34. data integration
  34. 35. expression data
  35. 36. cell cultures
  36. 38. synchronization
  37. 39. microarrays
  38. 41. time courses
  39. 43. expression profiles
  40. 45. list of genes
  41. 46. periodically expressed
  42. 47. S. cerevisiae
  43. 48. expression data
  44. 49. Cho et al.
  45. 50. Spellman et al.
  46. 51. computational methods
  47. 52. Zhao et al.
  48. 53. Langmead et al.
  49. 54. Johansson et al.
  50. 55. Wichert et al.
  51. 56. Luan and Li
  52. 57. Lu et al.
  53. 58. Ahdesm äki et al.
  54. 59. Willbrand et al.
  55. 60. Chen
  56. 61. Qiu et al.
  57. 62. Ahnert et al.
  58. 63. Glynn et al.
  59. 64. Andersson et al.
  60. 65. Lu et al.
  61. 66. Xu et al.
  62. 67. Liew et al.
  63. 68. no benchmarking
  64. 69. reanalysis
  65. 70. benchmarking
  66. 72. no progress
  67. 73. no benchmarking
  68. 74. S. pombe
  69. 75. H. sapiens
  70. 76. A. thaliana
  71. 77. reanalysis
  72. 78. benchmarking
  73. 79. list of genes
  74. 80. periodically expressed
  75. 81. four organisms
  76. 82. orthologous groups
  77. 83. sequence similarity
  78. 85. not conserved
  79. 86. others had seen the same
  80. 87. Ota et al.
  81. 88. Rustici et al.
  82. 89. Dyczkowski and Vingron
  83. 90. no explanation
  84. 91. a long time ago in a journal far, far away …
  85. 92. (Science, 2005)
  86. 93. temporal network
  87. 95. dynamic and static subunits
  88. 96. just-in-time assembly
  89. 98. evolutionary flexibility
  90. 99. different organisms
  91. 100. different dynamic subunits
  92. 101. manual curation
  93. 102. protein complexes
  94. 106. different time scales
  95. 107. time warping
  96. 108. same color = same phase
  97. 109. deoxynucleotide synthesis
  98. 111. dynamic subunits
  99. 112. time of peak expression
  100. 113. time of action
  101. 114. just-in-time assembly
  102. 116. CDK substrates
  103. 117. Phospho.ELM
  104. 118. Übersax et al.
  105. 119. Loog et al.
  106. 120. NetPhosK
  107. 121. correlation
  108. 123. Fisher’s exact test
  109. 125. cell cycle vs. non-cell cycle
  110. 126. correlated changes
  111. 128. Fisher’s exact test
  112. 130. co-evolution
  113. 131. transcriptional regulation
  114. 132. phosphorylation
  115. 133. targeted degradation
  116. 134. just-in-time assembly
  117. 136. summary
  118. 137. reanalysis
  119. 138. benchmarking
  120. 139. integration
  121. 140. high-throughput data
  122. 141. reproduce what is know
  123. 142. biological discoveries
  124. 143. testable hypotheses
  125. 144. protein complex regulation
  126. 145. evolution
  127. 146. Acknowledgments <ul><li>Thomas Skøt Jensen </li></ul><ul><li>Ulrik de Lichtenberg </li></ul><ul><li>Søren Brunak </li></ul><ul><li>Peer Bork </li></ul>
  128. 147. Thank you!
  129. 148. Questions?

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