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 this before
Ota et al.
Rustici et al.
Dyczkowski and Vingron
technical issues
orthology definitions
no reanalysis
different analysis methods
no error estimates
no biological explanation
turn back time …
temporal network
S. cerevisiae  cell cycle
 
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
DNA polymerases
 
dynamic subunits
time of peak expression
time of action
just-in-time assembly
 
CDK substrates
Übersax et al.
Loog et al.
Phospho.ELM
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
 
Acknowledgments <ul><li>Thomas Skøt Jensen </li></ul><ul><li>Ulrik de Lichtenberg </li></ul><ul><li>Søren Brunak </li></ul...
Thank you!
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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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MIPS Retreat, Kloster Frauenchiemsee, Chiemsee, Germany, July 9-10, 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 this before
  80. 87. Ota et al.
  81. 88. Rustici et al.
  82. 89. Dyczkowski and Vingron
  83. 90. technical issues
  84. 91. orthology definitions
  85. 92. no reanalysis
  86. 93. different analysis methods
  87. 94. no error estimates
  88. 95. no biological explanation
  89. 96. turn back time …
  90. 97. temporal network
  91. 98. S. cerevisiae cell cycle
  92. 100. dynamic and static subunits
  93. 101. just-in-time assembly
  94. 103. evolutionary flexibility
  95. 104. different organisms
  96. 105. different dynamic subunits
  97. 106. manual curation
  98. 107. protein complexes
  99. 111. different time scales
  100. 112. time warping
  101. 114. same color = same phase
  102. 115. DNA polymerases
  103. 117. dynamic subunits
  104. 118. time of peak expression
  105. 119. time of action
  106. 120. just-in-time assembly
  107. 122. CDK substrates
  108. 123. Übersax et al.
  109. 124. Loog et al.
  110. 125. Phospho.ELM
  111. 126. NetPhosK
  112. 127. correlation
  113. 129. Fisher’s exact test
  114. 131. cell cycle vs. non-cell cycle
  115. 132. correlated changes
  116. 134. Fisher’s exact test
  117. 136. co-evolution
  118. 137. transcriptional regulation
  119. 138. phosphorylation
  120. 139. targeted degradation
  121. 140. just-in-time assembly
  122. 142. 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>
  123. 143. Thank you!
  124. 144. Questions?

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