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Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
Protein networks as a scaffold for structuring other data
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Protein networks as a scaffold for structuring other data

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SEMM, IFOM, Milan, Italy, June 15-16, 2006

SEMM, IFOM, Milan, Italy, June 15-16, 2006

Published in: Technology
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Transcript

  • 1. Protein networks as a scaffold for structuring other data Lars Juhl Jensen EMBL Heidelberg
  • 2. cell cycle regulation
  • 3.  
  • 4. Chapter 1
  • 5. interaction networks
  • 6. what is an interaction?
  • 7. functional interactions
  • 8. physical interactions
  • 9. yeast two-hybrid
  • 10. complex pull-down
  • 11.  
  • 12. high-throughput
  • 13. S. cerevisiae
  • 14. Uetz et al.
  • 15. Ito et al.
  • 16. Gavin et al.
  • 17. Ho et al.
  • 18. Gavin et al.
  • 19. Krogan et al.
  • 20. C. elegans
  • 21. Li et al.
  • 22. D. melanogaster
  • 23. Giot et al.
  • 24. H. sapiens
  • 25. Stelzl et al.
  • 26. Rual et al.
  • 27.  
  • 28. yeehaa!
  • 29. network topology
  • 30. degree distribution
  • 31.  
  • 32. scale-free
  • 33.  
  • 34. hubs
  • 35. essentiality
  • 36. network robustness
  • 37. targeted attacks
  • 38. artefacts
  • 39. self-activating baits
  • 40. highly expressed proteins
  • 41. Han et al.
  • 42.  
  • 43. can we trust this data?
  • 44. the human interactome
  • 45. (incomplete)
  • 46. yeast two-hybrid
  • 47. 1936 13 4 4 1385 65 18465 Stelzl et al. Rual et al. Small-scale studies
  • 48. 32 0 3 4 18 4 23 Stelzl et al. Rual et al. Small-scale studies
  • 49. 62 8 39 Small-scale studies Stelzl et al. Rual et al. 852 17 473 432 69 260
  • 50. 3.5% and 21% sensitivity
  • 51. the yeast interactome
  • 52. five years ago
  • 53. yeast two-hybrid
  • 54. 1150 117 117 72 4053 118 4469 Uetz et al. Ito et al. Small-scale studies
  • 55. 162 53 34 72 180 29 338 Uetz et al. Ito et al. Small-scale studies
  • 56. 511 189 616 Small-scale studies Uetz et al. Ito et al. 439 178 759 897 190 1347
  • 57. 19% and 12% sensitivity
  • 58. three years ago
  • 59. complex pull-down
  • 60. 14186 784 1178 287 19492 230 3475 Gavin et al. Ho et al. Small-scale studies
  • 61. 2341 125 656 287 2725 42 149 Gavin et al. Ho et al. Small-scale studies
  • 62. 4431 1465 5041 Small-scale studies Gavin et al. Ho et al. 14913 1071 632 8047 517 746
  • 63. 63% and 41% sensitivity
  • 64. what about accuracy?
  • 65.  
  • 66.  
  • 67. 30–50% specificity
  • 68. what can we do about it?
  • 69. topology-based scoring
  • 70. complex pull-down
  • 71. log[(N 12 · N)/((N 1 +1) · (N 2 +1))]
  • 72. yeast two-hybrid
  • 73. -log((N 1 +1) · (N 2 +1))
  • 74. calibrate against KEGG
  • 75.  
  • 76. subcellular localization
  • 77.  
  • 78. filtering
  • 79. high-throughput
  • 80.  
  • 81. high-confidence
  • 82. Chapter 2
  • 83. expression data
  • 84. S. cerevisiae
  • 85.  
  • 86. synchronized cell culture
  • 87. microarray time series
  • 88.  
  • 89. periodically expressed genes
  • 90.  
  • 91. S. cerevisiae
  • 92. Cho et al.
  • 93. Spellman et al.
  • 94. yeehaa!
  • 95. Zhao et al.
  • 96. Langmead et al.
  • 97. Johansson et al.
  • 98. Wichert et al.
  • 99. Luan and Li
  • 100. Lu et al.
  • 101. Ahdesm äki et al.
  • 102. Willbrand et al.
  • 103. Chen et al.
  • 104. Qiu et al.
  • 105. Ahnert et al.
  • 106. Andersson et al.
  • 107. no benchmarking
  • 108. reanalysis
  • 109. benchmarking
  • 110.  
  • 111. no progress
  • 112. no benchmarking
  • 113.  
  • 114. Chapter 3
  • 115. 1+2 = 3
  • 116. expression data
  • 117.  
  • 118. protein interactions
  • 119.  
  • 120. temporal network
  • 121.  
  • 122. benchmarking
  • 123.  
  • 124.  
  • 125. very low error rate
  • 126. discovery tool
  • 127.  
  • 128. 30+ uncharacterized proteins
  • 129. detailed function prediction
  • 130. novel module
  • 131.  
  • 132. global statements
  • 133. dynamic and static
  • 134.  
  • 135.  
  • 136. CDK–cyclin complexes
  • 137.  
  • 138. consistent timing
  • 139.  
  • 140.  
  • 141. pre-replication complex
  • 142.  
  • 143. just-in-time assembly
  • 144.  
  • 145. how can we test this?
  • 146. evolutionary conservation
  • 147. Chapter 4
  • 148. more expression data
  • 149. S. cerevisiae
  • 150. microarray time series
  • 151.  
  • 152. periodically expressed genes
  • 153.  
  • 154. S. pombe
  • 155. Rustici et al.
  • 156. (good job)
  • 157. Peng et al.
  • 158. Oliva et al.
  • 159. no benchmarking
  • 160. no integration
  • 161. reanalysis
  • 162. benchmarking
  • 163.  
  • 164. no progress
  • 165. no benchmarking
  • 166. no integration
  • 167.  
  • 168. H. sapiens
  • 169. Whitfield et al.
  • 170. reanalysis
  • 171. benchmarking
  • 172.  
  • 173. A. thaliana
  • 174. Menges et al.
  • 175. reanalysis
  • 176. benchmarking
  • 177.  
  • 178. list of genes
  • 179. peak times
  • 180. Chapter 5
  • 181. cross-species comparison
  • 182. orthology assignment
  • 183. peak times
  • 184. not comparable
  • 185. time warping
  • 186.  
  • 187.  
  • 188. not conserved
  • 189. individual genes
  • 190. just-in-time assembly
  • 191. protein complexes
  • 192. DNA polymerases
  • 193.  
  • 194. pre-replication complex
  • 195.  
  • 196. chromatid cohesion
  • 197.  
  • 198. reproduces what is known
  • 199. known differences
  • 200. timing has changed
  • 201. identity has changed
  • 202. self-consistent
  • 203. make sense
  • 204. protein complexes
  • 205. individual genes
  • 206. broader perspective
  • 207. protein networks
  • 208. context
  • 209. understanding
  • 210. Acknowledgments Ulrik de Lichtenberg Thomas Skøt Jensen Christian von Mering Søren Brunak Peer Bork

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