1. Session outline 1.Standards and the problem of data integration Example: PSICQUIC and the PSICQUIC game 2.Introduction to ontologies. Exploring the Gene Ontology -Coffee break- 3.Introduction to protein-protein interactions (PPIs) IntAct: the molecular interactions database at the EBI -Lunch break- 4.Introduction to pathways Reactome: a database of human biological pathways -Coffee break- 5.Network representation and analysis: strategies and limitations Network generation and analysis through Cytoscape and PSICQUIC

2. Introduction to pathways

3. EMBL-EBI What are pathways? A set of bio-molecules that interact is called a: network > pathway > reaction > interaction/complex Biologists have been studying and modeling living systems for decades (physiology) –Q. What underlies the physiology? –A. Interactions between the molecules (and cells) A biological pathway is a model or abstraction of the functional relationships between the molecules that take part in a biological event.

4. EMBL-EBI What are pathways? Pathway vs Protein interaction network reflects scientific consensus reflects potential physical relation

5. EMBL-EBI What are pathways? “Model or abstraction of the functional relationships between the molecules that take part in a biological event” Generally pathways are a simple cascade of reactions leading to information flow e.g. adrenaline signalling, JAK-STAT pathway

6. EMBL-EBI Canonical Pathways The details of a named and characterized process Is it complete? Is it accurate? Does it show all the details? Can I see the evidence? Is this up to date? Can I export and reuse the steps?

7. EMBL-EBI Identifying New Pathways Mine existing data –Text or manually mine the literature –Annotate (manually or computationally) –Store in a useful way (database, exportable format) –e.g. KEGG, Ingenuity, Reactome Analysis and interpretation of new high-throughput data –Bioinformatics approaches for mining large datasets –Highly varied, no ‘right’ method, results often subjective! –e.g. Reactome Functional Interaction network Protein interaction networks Pathways

8. EMBL-EBI Pathway Databases KEGG – by subscription Reactome – free Ingenuity - commercial Metacore (GeneGO) – commercial Related databases –The Gene Ontology Project – free –TRANSFAC – commercial –BioModels - free

9. EMBL-EBI Pathway standards and tools Data exchange formats (XML based) –BioPax –SBML –CellML Modeling platforms –Cell Designer –BioUML Graphical representation –SBGN

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

11. www.reactome.org 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?

12. www.reactome.org 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?

13. www.reactome.org 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

14. www.reactome.org 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…

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

16. www.reactome.org Reaction Example 1: Enzymatic

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

18. www.reactome.org Other Reaction Types Binding Dimerization Phosphorylation

19. www.reactome.org Reactions Connect into Pathways OUTPUT INPUT CATALYST OUTPUT INPUT CATALYST INPUT OUTPUT CATALYST

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

21. www.reactome.org Species Selection Human-based 20 additional species computationally predicted

22. www.reactome.org 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

23. www.reactome.org 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

24. www.reactome.org Exportable Protein-Protein Interactions Inferred from complexes and reactions (more on this later) Interactions between proteins in the same complex, reaction, or adjoining reaction Lists available from Downloads See Readme document for more details

25. www.reactome.org Coverage – Content, TOC And many more...

26. www.reactome.org Planned Coverage – Editorial Calendar

27. www.reactome.org Reactome Tools Interactive Pathway Browser Analysis Pathway Mapping Over-representation Expression overlay Molecular Interaction overlay Biomart

28. www.reactome.org Tutorial Tutorial handouts in your info packages…

29. www.reactome.org Front Page http://www.reactome.org

30. www.reactome.org Exercise 1 …see the Tutorial handouts

31. www.reactome.org The Pathway Browser

32. www.reactome.org Pathway Hierarchy Panel Pathway Reaction Black-box

33. www.reactome.org Exercise 2 …see the Tutorial handouts

34. www.reactome.org 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

35. www.reactome.org Exercise 3 …see the Tutorial handouts

36. www.reactome.org Navigating in the Pathway Browser I Click here Highlights Details here Click here to open pathway diagram... Home button

37. www.reactome.org Details here Navigating in the Pathway Browser II Click hereZoomHighlights

38. www.reactome.org Exercise 4 …see the Tutorial handouts

39. www.reactome.org The Details Panel

40. www.reactome.org

41. Exercise 5 …see the Tutorial handouts

42. www.reactome.org Analysis – identifier list

43. www.reactome.org Overrepresentation P-vals

44. www.reactome.org Exercise 6 …see the Tutorial handouts

45. www.reactome.org Expression overlay I

46. www.reactome.org Expression overlay II

47. www.reactome.org Expression overlay III Yellow = high Blue = low Step through Data columns

48. www.reactome.org Exercise 7

49. www.reactome.org Species Comparison I Tools > Compare species

50. www.reactome.org Species Comparison II Yellow = human/rat Blue = human only No colour = no data

51. www.reactome.org Exercise 8 …see the Tutorial handouts

52. www.reactome.org Molecular Interaction Overlay

53. www.reactome.org Exercise 9 …see the Tutorial handouts

54. www.reactome.org End

55. www.reactome.org Acknowledgements & questions Steve Jupe Reactome project coordinator EBI-EMBL sjupe@ebi.ac.uk

56. www.reactome.org BioMart – selecting your dataset

57. www.reactome.org BioMart – filters

58. www.reactome.org BioMart – attributes Check to get attribute

59. www.reactome.org BioMart – results

60. www.reactome.org Exercise 10