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
transcription
interactions
phosphorylation
targeted degradation
S. cerevisiae
Cho et al.
Spellman et al.
microarrays
 
expression profiles
 
computational methods
Spellman et al.
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
cross-species comparison
reanalysis
S. pombe
H. sapiens
A. thaliana
400–600 periodic genes
four organisms
orthologous groups
 
not conserved
protein interactions
expression data
temporal network
 
dynamic and static subunits
just-in-time assembly
 
evolutionary flexibility
different organisms
different dynamic subunits
cross-species comparison
protein complexes
 
 
 
different time scales
time warping
 
DNA polymerases
 
different organisms
different dynamic subunits
time of peak expression
time of action
 
phosphorylation
Übersax et al.
Loog et al.
Phospho.ELM
NetPhosK
correlation
 
Fisher’s exact test
statistically significant
trivial
correlated changes
 
Fisher’s exact test
statistically significant
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...
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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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15th International Conference on Intelligent Systems for Molecular Biology, Austria Center Vienna, Vienna, Austria, July 22-25, 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. transcription
  17. 18. interactions
  18. 19. phosphorylation
  19. 20. targeted degradation
  20. 21. S. cerevisiae
  21. 22. Cho et al.
  22. 23. Spellman et al.
  23. 24. microarrays
  24. 26. expression profiles
  25. 28. computational methods
  26. 29. Spellman et al.
  27. 30. Zhao et al.
  28. 31. Langmead et al.
  29. 32. Johansson et al.
  30. 33. Wichert et al.
  31. 34. Luan and Li
  32. 35. Lu et al.
  33. 36. Ahdesm äki et al.
  34. 37. Willbrand et al.
  35. 38. Chen
  36. 39. Qiu et al.
  37. 40. Ahnert et al.
  38. 41. Glynn et al.
  39. 42. Andersson et al.
  40. 43. Lu et al.
  41. 44. Xu et al.
  42. 45. Liew et al.
  43. 46. no benchmarking
  44. 47. reanalysis
  45. 48. benchmarking
  46. 50. no progress
  47. 51. cross-species comparison
  48. 52. reanalysis
  49. 53. S. pombe
  50. 54. H. sapiens
  51. 55. A. thaliana
  52. 56. 400–600 periodic genes
  53. 57. four organisms
  54. 58. orthologous groups
  55. 60. not conserved
  56. 61. protein interactions
  57. 62. expression data
  58. 63. temporal network
  59. 65. dynamic and static subunits
  60. 66. just-in-time assembly
  61. 68. evolutionary flexibility
  62. 69. different organisms
  63. 70. different dynamic subunits
  64. 71. cross-species comparison
  65. 72. protein complexes
  66. 76. different time scales
  67. 77. time warping
  68. 79. DNA polymerases
  69. 81. different organisms
  70. 82. different dynamic subunits
  71. 83. time of peak expression
  72. 84. time of action
  73. 86. phosphorylation
  74. 87. Übersax et al.
  75. 88. Loog et al.
  76. 89. Phospho.ELM
  77. 90. NetPhosK
  78. 91. correlation
  79. 93. Fisher’s exact test
  80. 94. statistically significant
  81. 95. trivial
  82. 96. correlated changes
  83. 98. Fisher’s exact test
  84. 99. statistically significant
  85. 100. co-evolution
  86. 101. transcriptional regulation
  87. 102. phosphorylation
  88. 103. targeted degradation
  89. 104. just-in-time assembly
  90. 106. 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>
  91. 107. C1

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