1. www.reactome.org Murcia - 3 February 2011 1 A Database of human biological pathways Bijay Jassal

2. www.reactome.org Murcia - 3 February 2011 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 maybe reuse it?

3. www.reactome.org Murcia - 3 February 2011 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 Murcia - 3 February 2011 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 Murcia - 3 February 2011 5 Extensively cross-referenced Tools for data analysis – Pathway Analysis, Expression Overlay, Species Comparison, Biomart… Used to infer orthologous events in 20 non-human species Reactome is…

6. www.reactome.org Murcia - 3 February 2011 6 Theory - Reactions Pathway steps = the “units” of Reactome = events in biology TRANSPORT CLASSIC BIOCHEMICAL BINDING DISSOCIATION DEGRADATION PHOSPHORYLATION DEPHOSPHORYLATION

7. www.reactome.org Murcia - 3 February 2011 7 Reaction Example 1: Enzymatic

8. www.reactome.org Murcia - 3 February 2011 8 Reaction Example 2: Transport REACT_945.4 Transport of Ca++ from platelet dense tubular system to cytoplasm

9. www.reactome.org Murcia - 3 February 2011 9 Other Reaction Types Binding Dimerization Phosphorylation

10. www.reactome.org Murcia - 3 February 2011 10 Reactions Connect into Pathways OUTPUT INPUT CATALYST OUTPUT INPUT CATALYST INPUT OUTPUT CATALYST

11. www.reactome.org Murcia - 3 February 2011 11 Human pathway PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Evidence Tracking – Inferred Reactions

12. www.reactome.org Murcia - 3 February 2011 12 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

13. www.reactome.org Murcia - 3 February 2011 13 Species Selection

14. www.reactome.org Murcia - 3 February 2011 14 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

15. www.reactome.org Murcia - 3 February 2011 15 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

16. www.reactome.org Murcia - 3 February 2011 16 Coverage – Current TOC And many more...

17. www.reactome.org Murcia - 3 February 2011 17 Planned Coverage – Editorial Calendar

18. www.reactome.org Murcia - 3 February 2011 18 Reactome Tools Interactive Pathway Browser Pathway Mapping and Over-representation Expression overlay onto pathways Molecular Interaction overlay Biomart

19. www.reactome.org Murcia - 3 February 2011 19 Arabidopsis Reactome http://www.arabidopsisreactome.org/

20. www.reactome.org Murcia - 3 February 2011 20 Tutorial

21. www.reactome.org Murcia - 3 February 2011 21 Front Page http://www.reactome.org Sidebar Main text Navigation bar

22. www.reactome.org Murcia - 3 February 2011 22 Exercise 1

23. www.reactome.org Murcia - 3 February 2011 23 The Pathway Browser Species selector Search & Analyze bar Sidebar Pathway Diagram Panel Details Panel (hidden) Zoom/move toolbar Thumbnail

24. www.reactome.org Murcia - 3 February 2011 24 Pathways tab – pathway hierarchy Pathway Reaction Black-box

25. www.reactome.org Murcia - 3 February 2011 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 Murcia - 3 February 2011 26 The Pathway Browser - Pathway Diagrams Boxes are proteins, sets or complexes. Ovals are small molecules. 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 Murcia - 3 February 2011 27 Exercise 3 From the Homepage, search for the pathway ‘Effects of PIP2 hydrolysis’ and open it in the Pathway Browser. 1. What symbol represents the reaction for ‘Binding of IP3 to the IP3 receptor’? 2.2. What symbol represents the reaction ‘Transport of Ca++ from platelet dense tubular system to cytoplasm’? What subtype of reaction is this? 3.3. What is the catalyst (descriptive name) for ‘2-AG hydrolysis to arachidonate by MAGL’? Can you find its UniProt ID and name the two outputs of this reaction?

28. www.reactome.org Murcia - 3 February 2011 28 Navigating in the Pathway Browser I Click here Highlights Details here Click here to open pathway diagram... Home and Analyze buttons Search

29. www.reactome.org Murcia - 3 February 2011 29 HighlightsDetails here Navigating in the Pathway Browser II Click hereZoom

30. www.reactome.org Murcia - 3 February 2011 30 Exercise 4

31. www.reactome.org Murcia - 3 February 2011 31 The Details Panel

32. www.reactome.org Murcia - 3 February 2011 32 Exercise 5

33. www.reactome.org Murcia - 3 February 2011 33 Pathway Analysis

34. www.reactome.org Murcia - 3 February 2011 34 Pathway Analysis – Overrepresentation ‘Top-level’ Reveal next level P-val

35. www.reactome.org Murcia - 3 February 2011 35 Exercise 6 Check this! 1.What is the most significantly over-represented top-level pathway for this dataset? 2.How many genes are in this pathway, and how many were represented in the dataset? 3.Why is the top-level pathway Chromosome Maintenance higher in the list than Signalling by Wnt when the latter has a more significant probability score? (Hint – use the Open All button) 4.Can you interpret these results in terms of the underlying biology? (Hint: good luck, there are many correct answers!)

36. www.reactome.org Murcia - 3 February 2011 36 Species Comparison I

37. www.reactome.org Murcia - 3 February 2011 37 Species Comparison II Yellow = human/rat Blue = human only Grey = not relevant Black = Complex

38. www.reactome.org Murcia - 3 February 2011 38 Exercise 7

39. www.reactome.org Murcia - 3 February 2011 39 Expression Analysis I

40. www.reactome.org Murcia - 3 February 2011 40 Expression Analysis II ‘Hot’ = high ‘Cold’ = low Step through Data columns

41. www.reactome.org Murcia - 3 February 2011 41 Exercise 8

42. www.reactome.org Murcia - 3 February 2011 42 Molecular Interaction Overlay

43. www.reactome.org Murcia - 3 February 2011 43 Exercise 9 Open the pathway diagram for Netrin-1 Signaling. 1.Find the protein FADK1 (top centre of the cytosol). Right click on it and select Display Interactors. How many are there? 2.How many times has the interaction between FADK1 and Tumor endothelial marker 6 been documented? Hint: This detail is not in Reactome. 3.Find the protein SRC (to the left of FADK1). Display interactors for this protein. How many are there? Can you get a list of them? 4.Display interactors for UNC5B (bottom left of the cytosol). What happens and why? 5.What is the easiest way to remove interactors?

44. www.reactome.org Murcia - 3 February 2011 44 BioMart – selecting your dataset

45. www.reactome.org Murcia - 3 February 2011 45 BioMart – filters

46. www.reactome.org Murcia - 3 February 2011 46 BioMart – attributes Check to get attribute

47. www.reactome.org Murcia - 3 February 2011 47 BioMart – results

48. www.reactome.org Murcia - 3 February 2011 48 Exercise 10

49. www.reactome.org Murcia - 3 February 2011 49 The End