Making gene networks through data integration

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Making gene networks through data integration

  1. 1. Making gene networks through data integration Lars Juhl Jensen
  2. 2. association networks
  3. 3. guilt by association
  4. 4. molecular networks
  5. 5. proteins
  6. 6. string-db.org
  7. 7. small molecules
  8. 8. stitch-db.org
  9. 9. non-coding RNAs
  10. 10. compartments
  11. 11. compartments.jensenlab.org
  12. 12. tissues
  13. 13. tissues.jensenlab.org
  14. 14. diseases
  15. 15. data integration
  16. 16. computational predictions
  17. 17. gene neighborhood
  18. 18. Korbel et al., Nature Biotechnology, 2004
  19. 19. TargetScan
  20. 20. experimental data
  21. 21. gene expression
  22. 22. protein interactions
  23. 23. Jensen & Bork, Science, 2008
  24. 24. miRTarBase
  25. 25. curated knowledge
  26. 26. metabolic pathways
  27. 27. Letunic & Bork, Trends in Biochemical Sciences, 2008
  28. 28. signaling pathways
  29. 29. many databases
  30. 30. different formats
  31. 31. different identifiers
  32. 32. variable quality
  33. 33. not comparable
  34. 34. hard work
  35. 35. (Ph.D. students)
  36. 36. common identifiers
  37. 37. quality scores
  38. 38. von Mering et al., Nucleic Acids Research, 2005
  39. 39. score calibration
  40. 40. von Mering et al., Nucleic Acids Research, 2005
  41. 41. homology-based transfer
  42. 42. Franceschini et al., Nucleic Acids Research, 2013
  43. 43. missing most of the data
  44. 44. text mining
  45. 45. >10 km
  46. 46. too much to read
  47. 47. computer
  48. 48. as smart as a dog
  49. 49. teach it specific tricks
  50. 50. named entity recognition
  51. 51. comprehensive lexicon
  52. 52. let-7a-3p
  53. 53. let-7a*
  54. 54. flexible matching
  55. 55. let-7a
  56. 56. let7a
  57. 57. name expansions
  58. 58. let-7a
  59. 59. miR-let-7a
  60. 60. “black list”
  61. 61. SDS
  62. 62. co-mentioning
  63. 63. counting
  64. 64. within documents
  65. 65. within paragraphs
  66. 66. within sentences
  67. 67. high recall
  68. 68. high precision
  69. 69. fuzzy associations
  70. 70. NLP Natural Language Processing
  71. 71. Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]
  72. 72. extract stated facts
  73. 73. high precision
  74. 74. poor recall
  75. 75. Jensen et al., Nature Reviews Genetics, 2006
  76. 76. questions?

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