Making gene networks through data integration

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Lars Juhl Jensen

Korbel et al., Nature Biotechnology, 2004

Letunic & Bork, Trends in Biochemical Sciences, 2008

von Mering et al., Nucleic Acids Research, 2005

Franceschini et al., Nucleic Acids Research, 2013

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]

Jensen et al., Nature Reviews Genetics, 2006

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Making gene networks through data integration

1. Making gene networks through data integration Lars Juhl Jensen

2. association networks

3. guilt by association

5. molecular networks

6. proteins

11. compartments

12. compartments.jensenlab.org

13. tissues

14. tissues.jensenlab.org

15. diseases

16. data integration

17. computational predictions

18. gene neighborhood

19. Korbel et al., Nature Biotechnology, 2004

20. TargetScan

21. experimental data

22. gene expression

23.

24. protein interactions

25. Jensen & Bork, Science, 2008

26. miRTarBase

27. curated knowledge

28. metabolic pathways

29. Letunic & Bork, Trends in Biochemical Sciences, 2008

30. signaling pathways

31. many databases

32. different formats

33. different identifiers

34. variable quality

35. not comparable

36. hard work

37. (Ph.D. students)

38. common identifiers

39. quality scores

40. von Mering et al., Nucleic Acids Research, 2005

41. score calibration

42. von Mering et al., Nucleic Acids Research, 2005

43. homology-based transfer

44. Franceschini et al., Nucleic Acids Research, 2013

45. missing most of the data

46. text mining

47. >10 km

48. too much to read

49. computer

50. as smart as a dog

51. teach it specific tricks

52.

53.

54. named entity recognition

55. comprehensive lexicon

56. let-7a-3p

57. let-7a*

58. flexible matching

59. let-7a

60. let7a

61. name expansions

62. let-7a

63. miR-let-7a

64. “black list”

65. SDS

66. co-mentioning

67. counting

68. within documents

69. within paragraphs

70. within sentences

71.

72.

73. high recall

74. high precision

75. fuzzy associations

76. NLP Natural Language Processing

77. 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]

78. extract stated facts

79. high precision

80. poor recall

81. Jensen et al., Nature Reviews Genetics, 2006

82. questions?