PhenoMiner -integrating phenotype values for multiple strains

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Jennifer Smith

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Rat Genome Database rgd.mcw.edu PhenoMiner: Integrating Phenotype Measurement Values for Multiple Strains Mary Shimoyama XVIIIth International Workshop on Genetic Systems in the Rat – Kyoto, Japan

Standardized formats using ontologies for sample, measurement, method and experimental conditions

Comprehensive phenotype profiles for strains, substrains, congenics, knockouts, mutants

Public repository for researchers to post data – funding agency interest

Development of the rat phenome – linking phenotype to genotype,[object Object]

Sample Data Results Measurement and Methods

Sample Data Results Experimental Conditions Measurement and Methods

Compare a phenotype across ages for one or more strains

Compare phenotype values for a set of substrains

Comprehensive phenotype values for a single or multiple strains

Compare results from multiple methods ,[object Object]

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PhenoMiner -integrating phenotype values for multiple strains

1. Rat Genome Database rgd.mcw.edu PhenoMiner: Integrating Phenotype Measurement Values for Multiple Strains Mary Shimoyama XVIIIth International Workshop on Genetic Systems in the Rat – Kyoto, Japan

3. Standardized formats using ontologies for sample, measurement, method and experimental conditions

4. Data mining and presentation tool

5. Links to originating data sources

6. Comprehensive phenotype profiles for strains, substrains, congenics, knockouts, mutants

7. Public repository for researchers to post data – funding agency interest

9. Accessing PhenoMiner

10. Creating a Query

11. Creating a Query

12. Creating a Query

13. Creating a Query

14. Creating a Query

15. Creating a Query

16. Creating a Query

17. Creating a Query

18. Creating a Query

19. Creating a Query

20. Results

21. Results

22. Results

23. Results

24. Results

25. Sample Data Results

26. Sample Data Results

27. Sample Data Results Measurement and Methods

28. Sample Data Results Experimental Conditions Measurement and Methods

29.

30. Compare a phenotype across ages for one or more strains

31. Compare phenotype values for a set of substrains

32. Comprehensive phenotype values for a single or multiple strains

33.

34. Compare a phenotype across ages for one or more strains

35. Compare phenotype values for a set of substrains

36. Comprehensive phenotype values for a single or multiple strains

37.

38. Compare a phenotype across ages for one or more strains

39. Compare phenotype values for a set of substrains

40. Comprehensive phenotype values for a single or multiple strains

41.

42. Comprehensive phenotype values for a single or multiple strains

43.

44. Compare a phenotype across ages for one or more strains

45. Compare phenotype values for a set of substrains

46. Comprehensive phenotype values for a single or multiple strains

47.

48. Compare a phenotype across ages for one or more strains

49. Compare phenotype values for a set of substrains

50. Comprehensive phenotype values for a single or multiple strains

51.

52. Compare a phenotype across ages for one or more strains

53. Compare phenotype values for a set of substrains

54. Comprehensive phenotype values for a single or multiple strains

55.

56. Compare a phenotype across ages for one or more strains

57. Compare phenotype values for a set of substrains

58. Comprehensive phenotype values for a single or multiple strains

59.

60. Compare a phenotype across ages for one or more strains

61. Compare phenotype values for a set of substrains

62. Comprehensive phenotype values for a single or multiple strains

63.

64. Compare a phenotype across ages for one or more strains

65. Compare phenotype values for a set of substrains

66. Comprehensive phenotype values for a single or multiple strains

67.

68. Compare a phenotype across ages for one or more strains

69. Compare phenotype values for a set of substrains

70. Comprehensive phenotype values for a single or multiple strains

71.

72. Compare a phenotype across ages for one or more strains

73. Compare phenotype values for a set of substrains

74. Comprehensive phenotype values for a single or multiple strains

75. Compare results from multiple methods Fluid Filled Catheter Photoplethysmography, tail cuff Fluid Filled Catheter Isolated Perfused Heart

76.

77. NBRP data – complete integration of existing data, continued updates

78. Literature

79. integration of data from all QTL papers

80. integration of data from papers characterizing inbred, mutant, congenic and knockout strains

81.

82. Customization of bar charts

83. Side by side chart viewing

84. Dot plots for multiple phenotypes

85. Statistical analysis tools

86.

87. Direct links from QTL reports for parental, congenic strains

88. Links from strain variation tracks on Gbrowse

89.

90. Customization of bar charts

91. Side by side chart viewing

92. Dot plots for multiple phenotypes

93. Statistical analysis tools

94.

95. Direct links from QTL reports for parental, congenic strains

96. Links from strain variation tracks on Gbrowse

97. Links from SNPlotyperMamtr1 region

98. Acknowledgments RGD Howard Jacob Melinda Dwinell Diane Munzenmaier Elizabeth Worthey Shirng-Wern Tsaih Rajni Nigam Rene Lopez Stan Laulederkind Tom Hayman Tim Lowry Shur-jen Wang Jeff DePons Weisong Liu Pushkala Jayaraman NBRP TadaoSerikawa Takashi Kuramoto TomojiMashimo BirgerVoight Physgen Allen Cowley Howard Jacob Andrew Greene Julian Lombard David Mattson Anne Kwitek Melinda Dwinell Special Thanks to Rat Researchers worldwide! RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH Phenominer is funded by grant HL094271

PhenoMiner -integrating phenotype values for multiple strains

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