1. www.reactome.org June 2016 1 Welcome - webinar instructions All microphones will be muted whilst the trainer is speaking At the end of the presentation, we will take questions via the chat at the bottom of the GoToTraining panel. If you wish to ask a question, please use the “raise your hand” button and we can open your microphone. Please complete the feedback survey which will launch at the end of the webinar.

2. Webinar June 2016 The Reactome Pathway Database Steve Jupe

3. www.reactome.org June 2016 3 Overview Introduction Data Curation and Content Tools Pathway Browser Analysis Tools Summary Acknowledgements

4. www.reactome.org June 2016 4 Rationale – Journal information Nature 407(6805):770-6.The Biochemistry of Apoptosis. “Caspase-8 is the key initiator caspase in the death-receptor pathway. Upon ligand binding, death receptors such as CD95 (Apo-1/Fas) aggregate and form membrane- bound signalling complexes (Box 3). These complexes then recruit, through adapter proteins, several molecules of procaspase-8, resulting in a high local concentration of zymogen. The induced proximity model posits that under these crowded conditions, the low intrinsic protease activity of procaspase-8 (ref. 20) is sufficient to allow the various proenzyme molecules to mutually cleave and activate each other (Box 2). A similar mechanism of action has been proposed to mediate the activation of several other caspases, including caspase-2 and the nematode caspase CED-3 (ref. 21).” How can I access the pathway described here and reuse it?

5. www.reactome.org June 2016 5 Nature. 2000 Oct 12;407(6805):770-6. The biochemistry of apoptosis. Rationale - Figures “A picture paints a thousand words…” but… Not data, just pixels Omits key details Assumes familiarity Fact or hypothesis?

6. www.reactome.org June 2016 6 What is Reactome? Free open source human pathway knowledgebase Normal and disease-related pathways Mapped to cellular compartments Every event supported by published experiments (with citations). Authored by expert biologists, maintained by professional Curators Tools for data analysis and visualization Understanding gene lists or expression data in pathway context Downloads and RESTful API to support Computational Biology

7. www.reactome.org June 2016 7 Why Reactome? Reactions Pathway steps = Units of Reactome = biological event TRANSPORT CLASSIC BIOCHEMICAL BINDING DISSOCIATION DEGRADATION PHOSPHORYLATION DEPHOSPHORYLATION

8. www.reactome.org June 2016 8 Primary Sources (cross references) UniProt – proteins ChEBI – small molecules Ensembl – genes and transcripts RNA Central - ncRNAs PubMed – literature evidence GO Molecular Function Compartment Biological process

9. www.reactome.org June 2016 9 Reaction example 1: Enzymatic

10. www.reactome.org June 2016 10 Reaction example 2: Transport R-HSA-5694462.1 Transport of Ca++ from platelet dense tubular system to cytoplasm

11. www.reactome.org June 2016 11 Other reaction examples Binding Dimerization Phosphorylation

12. www.reactome.org June 2016 12 Reactions connect into Pathways OUTPUT INPUT CATALYST OUTPUT INPUT CATALYST INPUT OUTPUT CATALYST

13. www.reactome.org June 2016 13 Human pathway PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Evidence – Inferred Reactions

14. www.reactome.org June 2016 14 Pathways authored and reviewed by expert biologists Curator works with Author to represent knowledge in Reactome data structure New pathways sent for review by another expert New data release every 3 months Regular pathway updates. ORCID and used as attributions for Reactome content –For visibility of expert contributions (authors, reviewers and curators). Data Curation Process Curator ExpertReviewer

15. www.reactome.org June 2016 15 Species Selection

16. www.reactome.org June 2016 16 Data Expansion – Projecting to Other Species A + ATP A + ADP -P B Human A + ATP A + ADP -P B Mouse B A Drosophila Reaction not projected No orthologue - Protein not projected + ATP

17. www.reactome.org June 2016 17 Disease annotation in Reactome Three main areas: Infection (eg. HIV, influenza, botulism) microbially-expressed proteins Cancer (eg. EGFR, FGFR and NOTCH signalling) altered protein functions Metabolic diseases (eg. mucopolysaccharidoses, phenylketonuria, vitamin metabolism abnormalities) altered expression of proteins

18. www.reactome.org June 2016 18 Disease display in Reactome - Infection Host Interactions of HIV factors

19. www.reactome.org June 2016 19 Disease display in Reactome – Altered protein function in Cancer Constitutive Signaling by AKT1 E17K in Cancer

20. www.reactome.org June 2016 20 Disease display in Reactome – Loss of function in metabolism MPS IIID - Sanfilippo syndrome D

21. www.reactome.org June 2016 21 Downloads Pathways from Pathway Browser as text, PDF, etc. Entire database contents (and software) from Downloads page (linked to Homepage). Reusable standard formats BioPAX SBML UniProt to Pathways GO annotations Protein-Protein interaction pairs - Interactions between proteins in the same complex, reaction, or adjoining reaction

22. www.reactome.org June 2016 22 Contents Version 56 has annotations for: 9238 human proteins, 9422 complexes ~1800 small molecules, 9584 reactions, 2007 pathways, ~20,000 literature references.

23. www.reactome.org June 2016 23 Coverage – Content, TOC And many more...

24. www.reactome.org June 2016 24 Planned Coverage – Editorial Calendar

25. www.reactome.org June 2016 25 Reactome Tools Interactive Pathway Browser Analysis Over-representation Pathway topology Expression overlay Molecular interaction overlay Species comparison

26. www.reactome.org June 2016 26 Front Page http://www.reactome.org

27. www.reactome.org June 2016 27 Search Reactome

28. www.reactome.org June 2016 28 Search Reactome II

29. www.reactome.org June 2016 29 Search Reactome III

30. www.reactome.org June 2016 30 Search Reactome IV

31. www.reactome.org June 2016 31 Search Reactome V

32. www.reactome.org June 2016 32 The Pathway Browser HomeSpecies Layout Hierarchy Panel Thumbnail Zoom/Move Pathway Panel Detail Panel Fit to Page Open Diagram Video Tour Settings

33. www.reactome.org June 2016 33 Pathway Overview 33

34. www.reactome.org June 2016 34 Hierarchy Panel Pathway Reaction Black-box Inferred from New Updated Disease

35. www.reactome.org June 2016 35 The Pathway Browser - Pathway Diagrams Ovals are small molecules (or sets of) Green boxes are proteins, Blue are complexes, Blue with double-boundary are sets Transition Binding Dissociation Omitted Uncertain Regulation +ve -ve Catalyst Inputs Outputs Compartment Reaction node

36. www.reactome.org June 2016 36 Navigating in the Pathway Browser I Details here Home button Click reaction to open Click pathway to select, double-click to open diagram

37. www.reactome.org June 2016 37 Subpathway Highlighting

38. www.reactome.org June 2016 38 Details don’t update until selection Navigating in the Pathway Browser II Hover mouse HighlightsSelected

39. www.reactome.org June 2016 39 Navigating in the Pathway Browser III

40. www.reactome.org June 2016 40 Contextual Information Panel Names/IDsPin/Unpin

41. www.reactome.org June 2016 41 Interactors Click for Interactors Slide to FilterDownloadClick edge for evidence

42. www.reactome.org June 2016 42 Diagram Search

43. www.reactome.org June 2016 43 Colour Profiles

44. www.reactome.org June 2016 44 Diagram Key

45. www.reactome.org June 2016 45 Export Diagram

46. www.reactome.org June 2016 46 Show Illustration

47. www.reactome.org June 2016 47 The Details Panel - Overview Select Reveal Details Background Orthologues Key literature Before & After

48. www.reactome.org June 2016 48

49. www.reactome.org June 2016 49 Disease in Reactome Click here to display disease reaction Disease reaction overlaid on normal pathway Disease details

50. www.reactome.org June 2016 50 The Big List of Differentially Pathways and Experiment Expressed Molecules beyond….. Interpreting high-throughput data…Reactome Tools

51. www.reactome.org June 2016 51 Analysis

52. www.reactome.org June 2016 52 Analysis submission (identifier lists)

53. www.reactome.org June 2016 53 Analysis of identifier lists - Options

54. www.reactome.org June 2016 54 Analysis Result – Over-representation FDR

55. www.reactome.org June 2016 55 Analysis - Pathway topology matching

56. www.reactome.org June 2016 56 Expression overlay I

57. www.reactome.org June 2016 57 Expression overlay II Scaled to Data Step through Data columns Selected

58. www.reactome.org June 2016 58 Species Comparison I

59. www.reactome.org June 2016 59 Species Comparison II Yellow = orthologue No colour = not found OR no data

60. www.reactome.org June 2016 60 Molecular Interaction Overlay Click line… Zoom

61. www.reactome.org June 2016 61 Molecular Interaction Overlay - Data

62. www.reactome.org June 2016 62 Molecular Interaction Overlay – Set source

63. www.reactome.org June 2016 63 More Information From the Reactome Homepage Reactome User Guide help@reactome.org Tour Train Online - http://www.ebi.ac.uk/training/

64. www.reactome.org June 2016 64 Conclusions Reactome is a curated database of human biological pathways. Web site provides tools for visualizing and interpreting your experimental data. Downloadable as a data framework for systems biology modeling. All Reactome data and software are open, no licensing is required.

65. www.reactome.org June 2016 65 Acknowledgements

66. www.reactome.org June 2016 66 Thank you Questions, comments and suggestions help@reactome.org sjupe@ebi.ac.uk