1. Copyright OpenHelix. No use or reproduction without express written consent1

2. The Rat Genome Database (RGD) The Rat ( Rattus norvegicus ) Model Organism Database Materials prepared by: Cynthia Perreault-Micale, Ph.D. Dorothy S. Reilly, Ph.D. www.openhelix.com Updated: Q3 2010 Version 1

3. Copyright OpenHelix. No use or reproduction without express written consent3 RGD Agenda Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises The Rat Genome Database (RGD) http://rgd.mcw.edu/

4. Copyright OpenHelix. No use or reproduction without express written consent4 RGD http://pga.mcw.edu/ PhysGen: Knock-Out Rats for Physiological Genomics Rat Community Videos Latest News & Conference Watch http://rgd.mcw.edu

5. Copyright OpenHelix. No use or reproduction without express written consent5 History of RGD http://www.nature.com/ng/journal/v40/n5/index.html RGD: established September 1999 Links to more Info

6. Copyright OpenHelix. No use or reproduction without express written consent6 Genome Research11:1935, 2001 RGD Publications

7. Copyright OpenHelix. No use or reproduction without express written consent7 RGD Documentation & Help

8. Copyright OpenHelix. No use or reproduction without express written consent8 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

9. Copyright OpenHelix. No use or reproduction without express written consent9 The Rat Genome Database (RGD) http://rgd.mcw.edu/ Keyword Search Box Searching RGD Downloading & Search Features

10. Copyright OpenHelix. No use or reproduction without express written consent10 Input & Search Features Over 8.5 million terms ranked & indexed

11. Copyright OpenHelix. No use or reproduction without express written consent11 A Search Example arthritis

12. Copyright OpenHelix. No use or reproduction without express written consent12 RGD Search Results Annotations to these terms were found Matrix View Genes

13. Copyright OpenHelix. No use or reproduction without express written consent13 Genes Sort Export Refine

14. Copyright OpenHelix. No use or reproduction without express written consent14 RGD Gene Page Overview of Rat Ncf1 gene detail page We will enlarge & examine sections in the upcoming slides name, symbol, syn additional data database links sequence links references & history homologs comparative maps genome browsers ontologies & notes

15. Copyright OpenHelix. No use or reproduction without express written consent15 RGD Gene Page - Top Gene name and symbol Summary gene description Synonyms ArrayIDs Gene Type Related Sites with Links Additional data: candidate gene for quantitative trait loci (QTL), primer pairs, sequence tagged site (STS)

16. Copyright OpenHelix. No use or reproduction without express written consent16 RGD Gene Page – Homology & Maps Homologs Comparative Map Data Genome Browsers

17. Copyright OpenHelix. No use or reproduction without express written consent17 RGD Gene Page - Annotations Ontologies & Notes Database links Sequence links References Contact RGD

18. Copyright OpenHelix. No use or reproduction without express written consent18 Position Search – 3 Easy Steps First Search 1 3 2

19. Copyright OpenHelix. No use or reproduction without express written consent19 Results Export Position You can export these tables to a spreadsheet

20. Copyright OpenHelix. No use or reproduction without express written consent20 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

21. Copyright OpenHelix. No use or reproduction without express written consent21 RGD Data Types Genes QTLS Markers ESTS Maps Strains Ontologies Sequences References

22. Copyright OpenHelix. No use or reproduction without express written consent22 Gene Search calcitonin Previous search form Search Help Click here Set your limits Calcitonin, chromosome 1, rat genes only

23. Copyright OpenHelix. No use or reproduction without express written consent23 Gene Search Results Rat genes only, limited to chromosome 1 Search term – calcitonin Same format as we reviewed previously Click to reach gene record

24. Copyright OpenHelix. No use or reproduction without express written consent24 Rat QTL Search Joint/bone inflammation Previous search form Search Help Click here Limiting your search Same options for help & limits as gene search

25. Copyright OpenHelix. No use or reproduction without express written consent25 Rat QTL Results QTL Query Results for Joint/bone inflammation, chromosome 12, rat only Click Click on link to reach Cia25 QTL Report

26. Copyright OpenHelix. No use or reproduction without express written consent26 QTL Report Skip to any section of this report

27. Copyright OpenHelix. No use or reproduction without express written consent27 QTL Report, cont. Genome Data Annotations, etc.

28. Copyright OpenHelix. No use or reproduction without express written consent28 Strain Report

29. Copyright OpenHelix. No use or reproduction without express written consent29 RGD Strain Display Basic details: coat color, origin Annotations Ontologies Strain QTL data References

30. Copyright OpenHelix. No use or reproduction without express written consent30 Searching Strains & Other Data Types Are Easy

31. Copyright OpenHelix. No use or reproduction without express written consent31 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

32. Copyright OpenHelix. No use or reproduction without express written consent32 Genome Tools GBrowse VCMap SNPlotyper Gviewer BioMart RH Map Server ACP Haplotyper Genome Scanner Genome Conflicts

33. Copyright OpenHelix. No use or reproduction without express written consent33 About GBrowse Specify Search Add Tracks Display Settings Add Own Tracks

34. Copyright OpenHelix. No use or reproduction without express written consent34 About SNPlotyper http://www.snp-star.eu/ Select chromosome and region Select strains View haplotypes

35. Copyright OpenHelix. No use or reproduction without express written consent35 SNPlotyper

36. Copyright OpenHelix. No use or reproduction without express written consent36 View Haplotypes

37. Copyright OpenHelix. No use or reproduction without express written consent37 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

38. Copyright OpenHelix. No use or reproduction without express written consent38 Disease Portals RGD Disease Data Organized by disease topic New Topics being added Tutorial by RGD Obesity / Metabolic Cardiovascular Neurological Cancer

39. Copyright OpenHelix. No use or reproduction without express written consent39 Cardiovascular Disease Portal

40. Copyright OpenHelix. No use or reproduction without express written consent40 Cardiovascular Disease Portal, cont. Link to: Genes QTLs Strains Gene Ontology Overview Cellular Component Biological Process Molecular Function

41. Copyright OpenHelix. No use or reproduction without express written consent41 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

42. Copyright OpenHelix. No use or reproduction without express written consent42 Phenotypes & Models

43. Copyright OpenHelix. No use or reproduction without express written consent43 Phenotypes: Body Weight http://www.anim.med.kyoto-u.ac.jp/nbr/ http://pga.mcw.edu /

44. Copyright OpenHelix. No use or reproduction without express written consent44 Go to Strains & Models

45. Copyright OpenHelix. No use or reproduction without express written consent45 Strains & Models RGD Strain Search menu List of strains & vendors Disease Models Animal Husbandry Links to Reviews and more!

46. Copyright OpenHelix. No use or reproduction without express written consent46 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

47. Copyright OpenHelix. No use or reproduction without express written consent47 Pathways & Interactive Diagrams From homepage click on Pathways Top - Interactive Pathway Diagrams Lower - Pathways with terms linked to their ontology report Interactive Pathway Diagrams Pathways Metabolic Disease Regulatory Signaling http://rgd.mcw.edu/

48. Copyright OpenHelix. No use or reproduction without express written consent48 Interactive Pathway Diagrams Diagrams regularly added Links to genes & related pathways Description Linked Diagram Acronyms References & Import Key

49. Copyright OpenHelix. No use or reproduction without express written consent49 Pathways Also regulatory & signaling groups Explore any pathway from here

50. Copyright OpenHelix. No use or reproduction without express written consent50 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

51. Copyright OpenHelix. No use or reproduction without express written consent51 Community Nomenclature RGNC Rat Community Forums Resource Links RGD Labs

52. Copyright OpenHelix. No use or reproduction without express written consent52 RGD Labs Beta Tools News & Links Recent poster presentations Your feedback welcome

53. Copyright OpenHelix. No use or reproduction without express written consent53 Submit Data Contact info Nomenclature

54. Copyright OpenHelix. No use or reproduction without express written consent54 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

55. Copyright OpenHelix. No use or reproduction without express written consent55 Summary Detailed gene reports Extensive data & tools Multiple data types

56. Copyright OpenHelix. No use or reproduction without express written consent56 Summary: Portals Community Input is welcome Pathways

57. Copyright OpenHelix. No use or reproduction without express written consent57 RGD Agenda The Rat Genome Database (RGD) http://rgd.mcw.edu/ Introduction and Credits Basic Search and Gene Display QTLs and Other Data Types Genome Tools Disease Portals Phenotypes and Models Pathways Community Summary Exercises

58. Copyright OpenHelix. No use or reproduction without express written consent58