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

2. Reactome A Knowledgebase of Biological Processes Materials prepared by: Mary Mangan, Ph.D. Jennifer Williams, Ph.D. www.openhelix.com Updated: Q2 2011 Version 6

3. Copyright OpenHelix. No use or reproduction without express written consent3 Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises Introduction and Credits Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction Reactome: a knowledgebase of biological processes Curated by scientists Pathways, reactions, participants, and chemical entities http://www.reactome.org REACT_21369.1 - Interaction of MyoD:E protein with MEF2 MEF2 Classic site

5. Copyright OpenHelix. No use or reproduction without express written consent5 Reactome Credits Overview Reactome Team Scientific Advisory Board http://www.reactome.org/about.html

6. Copyright OpenHelix. No use or reproduction without express written consent6 Curation Information Reactome editors and Board choose topics Expert scientists: bench biologists author “modules”; like a mini-review Reactome staff check, refine, add Data is reviewed by peer reviewers, and periodically re- examined and updated

7. Copyright OpenHelix. No use or reproduction without express written consent7 Data Content Curation emphasis = human pathways Non-human data may be used to infer reactions Computationally predicted from human  others Species Comparison tool

8. Copyright OpenHelix. No use or reproduction without express written consent8 Table of Contents Overview of the whole collection New modules are indicated

9. Copyright OpenHelix. No use or reproduction without express written consent9 Editorial Calendar Planned future content You can add your input!

10. Copyright OpenHelix. No use or reproduction without express written consent10 Schema Details Data model for verbal description Schema for the “blueprint”

11. Copyright OpenHelix. No use or reproduction without express written consent11 User Guide and Literature User Guide available Citing page has references, and guide to citing Reactome See the Reactome references for additional detail http://pid.nci.nih.gov/PID/2007/ 071211/full/pid.2007.3.shtml

12. Copyright OpenHelix. No use or reproduction without express written consent12 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

13. Copyright OpenHelix. No use or reproduction without express written consent13 Reactome Homepage: www.reactome.org Pathway Analysis Navigation tabs Analysis Tools About Reactome Download Education Resources News & Notes Try this button Legacy Interface

14. Copyright OpenHelix. No use or reproduction without express written consent14 Keyword Basic Searches Enter keyword, search database Human-centric so first search defaults to Homo sapiens Can choose other species from results Sample query: cell cycle in Homo sapiens keyword cell cycle

15. Copyright OpenHelix. No use or reproduction without express written consent15 Results “cell cycle” query is displayed, can change species Keyword(s) highlighted Choices of data types to examine “Show” to view a specific results group Click to view record Many pages Results Categories “Show” a selected group of results

16. Copyright OpenHelix. No use or reproduction without express written consent16 Results - Proteins ProteinsShow Protein highlighted Protein details Links to other information Component of information Entity links Processes Change view

17. Copyright OpenHelix. No use or reproduction without express written consent17 Results - “Others” Others Activation Complex Literature Data

18. Copyright OpenHelix. No use or reproduction without express written consent18 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

19. Copyright OpenHelix. No use or reproduction without express written consent19 Pathway Browser click Search & Analyze Bar Details Panel (closed at first) Pathway Panel (empty) Cell cycle Sidebar (open)

20. Copyright OpenHelix. No use or reproduction without express written consent20 Pathway Browser: Searches click = pathway = single step reaction = 'black-box' reactions = molecule = complex http://www.reactome.org/userguide/Usersguide.html#The_Pathway_Browser

21. Copyright OpenHelix. No use or reproduction without express written consent21 Pathway Browser: Cell Cycle Display Zoom/move subpathwayNext slide Click to navigate view subpathways

22. Copyright OpenHelix. No use or reproduction without express written consent22 Pathway Browser: Cell Cycle Display Zoom/move http://www.reactome.org/userguide/Usersguide.html#Pathway_Diagrams

23. Copyright OpenHelix. No use or reproduction without express written consent23 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

24. Copyright OpenHelix. No use or reproduction without express written consent24 Additional Analysis Tools: Pathway Analysis www.reactome.org Analysis tools Map IDs to pathways Select file

25. Overrepresentation Copyright OpenHelix. No use or reproduction without express written consent25 Pathway Analysis: Overrepresentation Analysis Ordered hierarchy Overrepresented Pathways Table of Pathways Pathway Map Pathway Analysis help: http://www.reactome.org/userguide/Usersguide.html#Pathway_Analysis Reactions

26. Copyright OpenHelix. No use or reproduction without express written consent26 Species Comparison www.reactome.org select click Right click Color Legend: Yellow = shared Blue = human only Gray = no inference possible Black = complex

27. www.reactome.org Copyright OpenHelix. No use or reproduction without express written consent27 Expression Analysis click Observe the color changes

28. Copyright OpenHelix. No use or reproduction without express written consent28 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

29. Copyright OpenHelix. No use or reproduction without express written consent29 Advanced Search Extended search for more precision and complexity AND

30. Copyright OpenHelix. No use or reproduction without express written consent30 Advanced Search Example and Results Results link to pathways and entities in all species input output multi-species results obtained

31. Copyright OpenHelix. No use or reproduction without express written consent31 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

32. Copyright OpenHelix. No use or reproduction without express written consent32 Reactome BioMart Access Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org navigation bar

33. Copyright OpenHelix. No use or reproduction without express written consent33 Reactome Mart: Query Choices Regular query Help Canned queries

34. Copyright OpenHelix. No use or reproduction without express written consent34 Reactome Mart: Canned Query Search Choose query Run query Or upload files Enter pathways

35. Copyright OpenHelix. No use or reproduction without express written consent35 Canned Query Output Output tools The query details

36. Copyright OpenHelix. No use or reproduction without express written consent36 Regular Reactome Mart Query Choose database then dataset click UniProt IDs: P25445 P48023 P04637 P38936 P62993 P01112 P36507 P38398 P31749 click

37. Copyright OpenHelix. No use or reproduction without express written consent37 Regular Reactome Mart Query: Attributes

38. Copyright OpenHelix. No use or reproduction without express written consent38 Final query details First 10 query results Save/export results Links within Reactome and external resources Copyright OpenHelix. No use or reproduction without express written consent

39. 39 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

40. Copyright OpenHelix. No use or reproduction without express written consent40 Other Reactome Tools Search for a variety of small molecules PathFinder: illustrate connections between entities Functional Interaction (FI) Cytoscape Plugin Downloads—and a textbook!

41. Small Molecule Search Copyright OpenHelix. No use or reproduction without express written consent41 Help Combine search terms Draw your molecule

42. Small Molecule Search - Drawing Copyright OpenHelix. No use or reproduction without express written consent42 Drawing tools: Pulldown menus Drawing tools Bond tools Ring tools Element tools cholesterol

43. Small Molecule Search, cont. Copyright OpenHelix. No use or reproduction without express written consent43 Results for cholesterol search Lower search Create complex queries, on multiple categories of criteria: Formula, Mass, Charge, Ontology, & more Lower search interface

44. Copyright OpenHelix. No use or reproduction without express written consent44 PathFinder A sample start and end point shown

45. Copyright OpenHelix. No use or reproduction without express written consent45 PathFinder Results PathFinder presents items between two points start end paths found

46. Copyright OpenHelix. No use or reproduction without express written consent46 Reactome FI Cytoscape Plugin Cytoscape & Reactome plugin - download & install locally Plugin accesses Reactome’s Functional Interaction network Find pathway patterns related to cancer & other diseases http://genomebiology.com/content/11/5/R53

47. Copyright OpenHelix. No use or reproduction without express written consent47 Downloads Reactome data and code can be downloaded and used Variety of formats—even a textbook! Can set up your own local copy textbook

48. Copyright OpenHelix. No use or reproduction without express written consent48 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

49. http://www.reactome.org Copyright OpenHelix. No use or reproduction without express written consent49 Entity pages Summary Reactome: for pathways and entities Tools and views to find and visualize what you need Pathway displays BioMart

50. Copyright OpenHelix. No use or reproduction without express written consent50 Reactome Agenda Reactome Pathway Knowledgebase: http://www.reactome.orghttp://www.reactome.org Introduction and Credits Basic Keyword Search Pathway Browser Additional Analysis Tools Advanced Search Reactome BioMart Other Reactome Tools Summary Exercises

51. Copyright OpenHelix. No use or reproduction without express written consent51