PhenoMiner -integrating phenotype values for multiple strains

530 views

Published on

Published in: Technology
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
530
On SlideShare
0
From Embeds
0
Number of Embeds
86
Actions
Shares
0
Downloads
5
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

PhenoMiner -integrating phenotype values for multiple strains

  1. 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
  2. 2. PhenoMiner Project Integrates phenotype data from multiple sources: Physgen, NBRP, Literature, Direct Submission Standardized formats using ontologies for sample, measurement, method and experimental conditions Data mining and presentation tool Links to originating data sources 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
  3. 3. Accessing PhenoMiner
  4. 4. Accessing PhenoMiner
  5. 5. Creating a Query
  6. 6. Creating a Query
  7. 7. Creating a Query
  8. 8. Creating a Query
  9. 9. Creating a Query
  10. 10. Creating a Query
  11. 11. Creating a Query
  12. 12. Creating a Query
  13. 13. Creating a Query
  14. 14. Creating a Query
  15. 15. Results
  16. 16. Results
  17. 17. Results
  18. 18. Results
  19. 19. Results
  20. 20. Sample Data Results
  21. 21. Sample Data Results
  22. 22. Sample Data Results Measurement and Methods
  23. 23. Sample Data Results Experimental Conditions Measurement and Methods
  24. 24. Uses Compare phenotypes across experiments for one or more strains 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
  25. 25. Uses Compare phenotypes across experiments for one or more strains 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
  26. 26. Uses Compare phenotypes across experiments for one or more strains 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
  27. 27. Uses Compare phenotypes across experiments for one or more strains 70 days Compare a phenotype across ages for one or more strains 42 days 35 days Compare phenotype values for a set of substrains Comprehensive phenotype values for a single or multiple strains Compare results from multiple methods
  28. 28. Uses Compare phenotypes across experiments for one or more strains 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
  29. 29. Uses Compare phenotypes across experiments for one or more strains 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
  30. 30. Uses Compare phenotypes across experiments for one or more strains 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
  31. 31. Uses Compare phenotypes across experiments for one or more strains 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
  32. 32. Uses Compare phenotypes across experiments for one or more strains 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
  33. 33. Uses Compare phenotypes across experiments for one or more strains 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
  34. 34. Uses Compare phenotypes across experiments for one or more strains 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
  35. 35. Uses Compare phenotypes across experiments for one or more strains 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 Fluid Filled Catheter Photoplethysmography, tail cuff Fluid Filled Catheter Isolated Perfused Heart
  36. 36. Future Developments Data Physgen data – complete integration NBRP data – complete integration of existing data, continued updates Literature integration of data from all QTL papers integration of data from papers characterizing inbred, mutant, congenic and knockout strains Researcher submissions – completion of online software for data submission
  37. 37. Future Developments Data Mining and Visualization Improved searching and query building Customization of bar charts Side by side chart viewing Dot plots for multiple phenotypes Statistical analysis tools Uploading and visualization of own data Links with Other Tools Direct links from strain reports, strain medical records Direct links from QTL reports for parental, congenic strains Links from strain variation tracks on Gbrowse Links from SNPlotyper
  38. 38. Future Developments Data Mining and Visualization Improved searching and query building Customization of bar charts Side by side chart viewing Dot plots for multiple phenotypes Statistical analysis tools Uploading and visualization of own data Links with Other Tools Direct links from strain reports, strain medical records Direct links from QTL reports for parental, congenic strains Links from strain variation tracks on Gbrowse Links from SNPlotyper Mamtr1 region
  39. 39. 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

×