Protein networks as a scaffold for structuring other data
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SEMM, IFOM, Milan, Italy, June 15-16, 2006
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Protein networks as a scaffold for structuring other data
- 1. Protein networks as a scaffold for structuring other data Lars Juhl Jensen EMBL Heidelberg
- 4. Chapter 1
- 6. what is an interaction?
- 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.
- 28. yeehaa!
- 29. network topology
- 32. scale-free
- 34. hubs
- 35. essentiality
- 37. targeted attacks
- 38. artefacts
- 41. Han et al.
- 43. can we trust this data?
- 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
- 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
- 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
- 68. what can we do about it?
- 71. log[(N 12 · N)/((N 1 +1) · (N 2 +1))]
- 72. yeast two-hybrid
- 73. -log((N 1 +1) · (N 2 +1))
- 78. filtering
- 79. high-throughput
- 81. high-confidence
- 82. Chapter 2
- 83. expression data
- 84. S. cerevisiae
- 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
- 111. no progress
- 112. no benchmarking
- 114. Chapter 3
- 115. 1+2 = 3
- 116. expression data
- 118. protein interactions
- 120. temporal network
- 122. benchmarking
- 125. very low error rate
- 126. discovery tool
- 130. novel module
- 132. global statements
- 133. dynamic and static
- 136. CDK–cyclin complexes
- 138. consistent timing
- 145. how can we test this?
- 147. Chapter 4
- 148. more expression data
- 149. S. cerevisiae
- 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
- 164. no progress
- 165. no benchmarking
- 166. no integration
- 168. H. sapiens
- 169. Whitfield et al.
- 170. reanalysis
- 171. benchmarking
- 173. A. thaliana
- 174. Menges et al.
- 175. reanalysis
- 176. benchmarking
- 178. list of genes
- 179. peak times
- 180. Chapter 5
- 182. orthology assignment
- 183. peak times
- 184. not comparable
- 185. time warping
- 188. not conserved
- 189. individual genes
- 191. protein complexes
- 192. DNA polymerases
- 196. chromatid cohesion
- 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