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

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