0
Just-in-time assembly The evolution of transcriptional and post-translational cell-cycle regulation of protein complexes L...
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.
Andersson et al.
Lu et al.
no benchmarking
reanalysis
benchmarking
 
no progress
no benchmarking
protein interactions
S. cerevisiae
Uetz et al.
Ito et al.
Gavin et al.
Ho et al.
topology-based scoring
quality threshold
subcellular localization
expression data
temporal network
 
benchmarking
 
 
30–50% false positives
 
3–5% false positives
detailed function prediction
uncharacterized proteins
who
whom
when
global statements
consistent timing
 
 
dynamic and static
 
 
just-in-time assembly
partial protein complexes
last missing subunits
post-translational regulation
phosphorylation
Übersax et al.
27% of dynamic proteins
8% of static proteins
targeted degradation
PEST regions
44% of dynamic proteins
29% of static proteins
undescribed link
transcriptional regulation
post-translational regulation
how can we test this?
cross-species comparison
evolutionary conservation
expression data
S. pombe
Rustici et al.
Peng et al.
Oliva et al.
no benchmarking
no integration
reanalysis
integration
benchmarking
 
no progress
no benchmarking
no integration
H. sapiens
Whitfield et al.
reanalysis
benchmarking
 
A. thaliana
Menges et al.
reanalysis
benchmarking
 
four organisms
list of genes
periodically expressed
orthology detection
sequence similarity
 
not conserved
individual genes
just-in-time assembly
protein complexes
 
 
 
 
different time scales
time warping
 
same color = same phase
just-in-time assembly
DNA polymerases
 
deoxynucleotide synthesis
 
phosphorylation
Übersax et al.
Loog et al.
Phospho.ELM
NetPhosK
correlation
 
 
cell cycle vs. non-cell cycle
co-evolution
 
 
transcriptional regulation
post-translational regulation
co-evolution
just-in-time assembly
multi-layer regulation
evolutionary flexibility
protein complexes
 
summary
reanalysis
integration
high-throughput data
reproduce what is know
biological discoveries
testable hypotheses
evolutionary conservation
Acknowledgments <ul><li>Thomas Skøt Jensen </li></ul><ul><li>Ulrik de Lichtenberg </li></ul><ul><li>Søren Brunak </li></ul...
Questions?
Upcoming SlideShare
Loading in...5
×

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

340

Published on

University of Natural Resources and Applied Life Sciences, Vienna, Austria, February 15, 2007

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
340
On Slideshare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
13
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

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

  1. 1. Just-in-time assembly The 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. Andersson et al.
  59. 64. Lu et al.
  60. 65. no benchmarking
  61. 66. reanalysis
  62. 67. benchmarking
  63. 69. no progress
  64. 70. no benchmarking
  65. 71. protein interactions
  66. 72. S. cerevisiae
  67. 73. Uetz et al.
  68. 74. Ito et al.
  69. 75. Gavin et al.
  70. 76. Ho et al.
  71. 77. topology-based scoring
  72. 78. quality threshold
  73. 79. subcellular localization
  74. 80. expression data
  75. 81. temporal network
  76. 83. benchmarking
  77. 86. 30–50% false positives
  78. 88. 3–5% false positives
  79. 89. detailed function prediction
  80. 90. uncharacterized proteins
  81. 91. who
  82. 92. whom
  83. 93. when
  84. 94. global statements
  85. 95. consistent timing
  86. 98. dynamic and static
  87. 101. just-in-time assembly
  88. 102. partial protein complexes
  89. 103. last missing subunits
  90. 104. post-translational regulation
  91. 105. phosphorylation
  92. 106. Übersax et al.
  93. 107. 27% of dynamic proteins
  94. 108. 8% of static proteins
  95. 109. targeted degradation
  96. 110. PEST regions
  97. 111. 44% of dynamic proteins
  98. 112. 29% of static proteins
  99. 113. undescribed link
  100. 114. transcriptional regulation
  101. 115. post-translational regulation
  102. 116. how can we test this?
  103. 117. cross-species comparison
  104. 118. evolutionary conservation
  105. 119. expression data
  106. 120. S. pombe
  107. 121. Rustici et al.
  108. 122. Peng et al.
  109. 123. Oliva et al.
  110. 124. no benchmarking
  111. 125. no integration
  112. 126. reanalysis
  113. 127. integration
  114. 128. benchmarking
  115. 130. no progress
  116. 131. no benchmarking
  117. 132. no integration
  118. 133. H. sapiens
  119. 134. Whitfield et al.
  120. 135. reanalysis
  121. 136. benchmarking
  122. 138. A. thaliana
  123. 139. Menges et al.
  124. 140. reanalysis
  125. 141. benchmarking
  126. 143. four organisms
  127. 144. list of genes
  128. 145. periodically expressed
  129. 146. orthology detection
  130. 147. sequence similarity
  131. 149. not conserved
  132. 150. individual genes
  133. 151. just-in-time assembly
  134. 152. protein complexes
  135. 157. different time scales
  136. 158. time warping
  137. 160. same color = same phase
  138. 161. just-in-time assembly
  139. 162. DNA polymerases
  140. 164. deoxynucleotide synthesis
  141. 166. phosphorylation
  142. 167. Übersax et al.
  143. 168. Loog et al.
  144. 169. Phospho.ELM
  145. 170. NetPhosK
  146. 171. correlation
  147. 174. cell cycle vs. non-cell cycle
  148. 175. co-evolution
  149. 178. transcriptional regulation
  150. 179. post-translational regulation
  151. 180. co-evolution
  152. 181. just-in-time assembly
  153. 182. multi-layer regulation
  154. 183. evolutionary flexibility
  155. 184. protein complexes
  156. 186. summary
  157. 187. reanalysis
  158. 188. integration
  159. 189. high-throughput data
  160. 190. reproduce what is know
  161. 191. biological discoveries
  162. 192. testable hypotheses
  163. 193. evolutionary conservation
  164. 194. 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>
  165. 195. Questions?
  1. A particular slide catching your eye?

    Clipping is a handy way to collect important slides you want to go back to later.

×