1. www.reactome.org May 2012 1 A Database of human biological pathways Steve Jupe - sjupe@ebi.ac.uk

2. www.reactome.org May 2012 2 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?

3. www.reactome.org May 2012 3 Nature. 2000 Oct 12;407(6805):770-6. The biochemistry of apoptosis. Rationale - Figures A picture paints a thousand words… but…. Just pixels Omits key details Assumes Fact or Hypothesis?

4. www.reactome.org May 2012 4 Reactome is… Free, online, open-source curated database of pathways and reactions in human biology Authored by expert biologists, maintained by Reactome editorial staff (curators) Mapped to cellular compartment

5. www.reactome.org May 2012 5 Extensively cross-referenced Tools for data analysis – Pathway Analysis, Expression Overlay, Species Comparison, Biomart… Used to infer orthologous events in 20 other species Reactome is…

6. www.reactome.org May 2012 6 human PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Using model organism data to build pathways – Inferred pathway events

7. www.reactome.org May 2012 7 Theory - Reactions Pathway steps = the “units” of Reactome = events in biology TRANSPORT CLASSIC BIOCHEMICAL BINDING DISSOCIATION DEGRADATION PHOSPHORYLATION DEPHOSPHORYLATION

8. www.reactome.org May 2012 8 Reaction Example 1: Enzymatic

9. www.reactome.org May 2012 9 Reaction Example 2: Transport REACT_945.4 Transport of Ca++ from platelet dense tubular system to cytoplasm

10. www.reactome.org May 2012 10 Other Reaction Types Binding Dimerization Phosphorylation

11. www.reactome.org May 2012 11 Reactions Connect into Pathways OUTPUT INPUT CATALYST OUTPUT INPUT CATALYST INPUT OUTPUT CATALYST

12. www.reactome.org May 2012 12 Human pathway PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Evidence Tracking – Inferred Reactions

13. www.reactome.org May 2012 13 Data Expansion - Link-outs From Reactome GO Molecular Function Compartment Biological process KEGG, ChEBI – small molecules UniProt – proteins Sequence dbs – Ensembl, OMIM, Entrez Gene, RefSeq, HapMap, UCSC, KEGG Gene PubMed references – literature evidence for events

14. www.reactome.org May 2012 14 Species Selection

15. www.reactome.org May 2012 15 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 inferred No orthologue - Protein not inferred + ATP

16. www.reactome.org May 2012 16 Exportable Protein-Protein Interactions Inferred from complexes and reactions Interactions between proteins in the same complex, reaction, or adjoining reaction Lists available from Downloads See Readme document for more details

17. www.reactome.org May 2012 17 Coverage – Content, TOC And many more...

18. www.reactome.org May 2012 18 Planned Coverage – Editorial Calendar

19. www.reactome.org May 2012 19 Reactome Tools Interactive Pathway Browser Pathway Mapping and Over-representation Expression overlay onto pathways Molecular Interaction overlay Biomart

20. www.reactome.org May 2012 20 Tutorial

21. www.reactome.org May 2012 21 Front Page http://www.reactome.org Sidebar Main text Navigation bar

22. www.reactome.org May 2012 22 Exercise 1

23. www.reactome.org May 2012 23 The Pathway Browser Species selector Diagram Key Sidebar Pathway Diagram Panel Details Panel (hidden) Zoom/move toolbar Thumbnail

24. www.reactome.org May 2012 24 Pathways tab – pathway hierarchy Pathway Reaction Black-box

25. www.reactome.org May 2012 25 Exercise 2 From the homepage, search for ‘Notch signaling’. Click on the top pathway hit. This will open it in the Pathway Browser. Ignoring the diagram for now, look at the Pathways tab on the left. 1.How many sub-pathways does this pathway have? 2.How many reactions are in the first of these sub-pathways? 3.What reaction follows Notch 2 precursor transport to Golgi? Hint: If it’s not visible, open the Details pane at the bottom of the page by clicking on the blue triangle.

26. www.reactome.org May 2012 26 The Pathway Browser - Pathway Diagrams Boxes are proteins, protein sets, mixed sets or complexes. Ovals are small molecules (or sets of) Green boxes are proteins or sets, blue are complexes. Catalyst Input Outputs Compartment Reaction node Transition Binding Dissociation Omitted Uncertain Regulation +ve -ve

27. www.reactome.org May 2012 27 Exercise 3

28. www.reactome.org May 2012 28 Navigating in the Pathway Browser I Click here Highlights Details here Click here to open pathway diagram... Home and Analyze buttons

29. www.reactome.org May 2012 29 Details here Navigating in the Pathway Browser II Click hereZoomHighlights

30. www.reactome.org May 2012 30 Exercise 4

31. www.reactome.org May 2012 31 The Details Panel

32. www.reactome.org May 2012 32 Exercise 5

33. www.reactome.org May 2012 33 Pathway Analysis

34. www.reactome.org May 2012 34 Pathway Analysis – Overrepresentation ‘Top-level’ Reveal next level P-val

35. www.reactome.org May 2012 35 Exercise 6 Check this!

36. www.reactome.org May 2012 36 Species Comparison I

37. www.reactome.org May 2012 37 Species Comparison II Yellow = human/rat Blue = human only Grey = not relevant Black = Complex

38. www.reactome.org May 2012 38 Exercise 7

39. www.reactome.org May 2012 39 Expression Analysis I

40. www.reactome.org May 2012 40 Expression Analysis II ‘Hot’ = high ‘Cold’ = low Step through Data columns

41. www.reactome.org May 2012 41 Exercise 8

42. www.reactome.org May 2012 42 Molecular Interaction Overlay

43. www.reactome.org May 2012 43 Exercise 9

44. www.reactome.org May 2012 44 The End

45. www.reactome.org May 2012 45 BioMart – selecting your dataset

46. www.reactome.org May 2012 46 BioMart – filters

47. www.reactome.org May 2012 47 BioMart – attributes Check to get attribute

48. www.reactome.org May 2012 48 BioMart – results

49. www.reactome.org May 2012 49 Exercise 10