Protein interaction networks

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Protein interaction networks

  1. 1. Protein interaction networks Lars Juhl Jensen
  2. 2. structure of interactions
  3. 3. physical networks
  4. 4. association networks
  5. 5. STRING
  6. 6. the cell cycle
  7. 7. essential process
  8. 8. grow and divide
  9. 9. one cell
  10. 10. two cells
  11. 11. four phases
  12. 12. G 1 phase
  13. 13. growth
  14. 14. S phase
  15. 15. DNA replication
  16. 16. G 2 phase
  17. 17. growth
  18. 18. M phase
  19. 19. cell division
  20. 21. regulation
  21. 22. gene expression
  22. 23. phosphorylation
  23. 24. targeted degradation
  24. 25. protein interactions
  25. 26. exercise 1
  26. 27. http://string-db.org
  27. 28. Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
  28. 31. association networks
  29. 32. guild by association
  30. 34. STRING
  31. 35. >1100 genomes
  32. 36. genomic context
  33. 37. gene fusion
  34. 38. Korbel et al., Nature Biotechnology , 2004
  35. 39. conserved neighborhood
  36. 40. Korbel et al., Nature Biotechnology , 2004
  37. 41. phylogenetic profiles
  38. 42. Korbel et al., Nature Biotechnology , 2004
  39. 43. protein interactions
  40. 44. Jensen & Bork, Science , 2008
  41. 45. genetic interactions
  42. 46. Beyer et al., Nature Reviews Genetics , 2007
  43. 47. gene coexpression
  44. 49. curated knowledge
  45. 50. Letunic & Bork, Trends in Biochemical Sciences , 2008
  46. 51. >10 km
  47. 52. text mining
  48. 53. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
  49. 54. co-mentioning
  50. 55. NLP Natural Language Processing
  51. 56. different sources
  52. 57. Ensembl
  53. 58. RefSeq
  54. 59. BIND Biomolecular Interaction Network Database
  55. 60. BioGRID General Repository for Interaction Datasets
  56. 61. DIP Database of Interacting Proteins
  57. 62. IntAct
  58. 63. MINT Molecular Interactions Database
  59. 64. HPRD Human Protein Reference Database
  60. 65. PDB Protein Data Bank
  61. 66. GEO Gene Expression Omnibus
  62. 67. MIPS Munich Information center for Protein Sequences
  63. 68. Gene Ontology
  64. 69. BioCyc
  65. 70. KEGG Kyoto Encyclopedia of Genes and Genomes
  66. 71. PID NCI-Nature Pathway Interaction Database
  67. 72. Reactome
  68. 73. different formats
  69. 74. different names
  70. 75. CDC2
  71. 76. CDK1
  72. 77. P06493
  73. 78. not comparable
  74. 79. variable quality
  75. 81. confidence scores
  76. 82. von Mering et al., Nucleic Acids Research , 2005
  77. 83. transfer by orthology
  78. 84. von Mering et al., Nucleic Acids Research , 2005
  79. 85. combine scores
  80. 86. exercise 2
  81. 87. you are probably here
  82. 90. high confidence only
  83. 92. experiments only
  84. 94. evidence viewers
  85. 96. cell cycle analysis
  86. 97. gene expression
  87. 98. cell cultures
  88. 99. synchronization
  89. 100. microarrays
  90. 102. time courses
  91. 103. Gauthier et al., Nucleic Acids Research , 2007
  92. 104. cycling genes
  93. 105. time of peak expression
  94. 107. protein interactions
  95. 108. temporal network
  96. 109. de Lichtenberg, Jensen et al., Science , 2005
  97. 110. just-in-time assembly
  98. 111. de Lichtenberg, Jensen et al., Cell Cycle , 2007
  99. 112. evolutionary flexibility
  100. 113. orthologs and paralogs
  101. 114. protein complexes
  102. 116. exercise 3
  103. 118. http://string-db.org
  104. 121. network expansion
  105. 124. what is known
  106. 126. external data
  107. 127. save network
  108. 129. open in Cytoscape
  109. 130. layout
  110. 131. clustering
  111. 132. project data onto network
  112. 133. de Lichtenberg, Jensen et al., Science , 2005
  113. 134. very flexible
  114. 135. lose the STRING interface
  115. 136. payload mechanism
  116. 137. show external data
  117. 138. nodes
  118. 139. edges
  119. 140. hosted on your server
  120. 141. exercise 4
  121. 143. http://cyclebase-string.jensenlab.org
  122. 146. network expansion
  123. 148. CDK–cyclin complexes
  124. 151. chemical networks
  125. 152. STITCH
  126. 153. STRING + chemicals
  127. 154. PubChem compounds
  128. 155. >74,000 small molecules
  129. 156. experimental data
  130. 157. BindingDB
  131. 158. ChEMBL
  132. 159. PDSP K i Psycoactive Drug Screening Program
  133. 160. PDB Protein Data Bank
  134. 161. drug targets
  135. 162. CTD Comparative Toxicogenomics Database
  136. 163. DrugBank
  137. 164. GLIDA GPCR-Ligand Database
  138. 165. Matador
  139. 166. TTD Therapeutic Target Database
  140. 167. metabolic pathways
  141. 168. BioCyc
  142. 169. KEGG Kyoto Encyclopedia of Genes and Genomes
  143. 170. Reactome
  144. 171. exercise 5
  145. 174. http://stitch-db.org
  146. 175. Kuhn et al., Nucleic Acids Research , 2010
  147. 178. what is known
  148. 180. thank you!

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