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A Database of human biological pathways Janna Hastings James Watson

A Database of human biological pathways Janna Hastings James Watson. Rationale – Journal information. Nature 407(6805):770-6.The Biochemistry of Apoptosis.

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A Database of human biological pathways Janna Hastings James Watson

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  1. A Database of human biological pathways Janna Hastings James Watson

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

  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. Reactome is… Extensively cross-referenced Tools for data analysis – Pathway Analysis, Expression Overlay, Species Comparison, Biomart… Used to infer orthologous events in 20 non-human species

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

  7. Reaction Example 1: Enzymatic

  8. Reaction Example 2: Transport Transport of Ca++ from platelet dense tubular system to cytoplasm REACT_945.4

  9. Other Reaction Types Dimerization Binding Phosphorylation

  10. Reactions Connect into Pathways CATALYST CATALYST CATALYST INPUT OUTPUT INPUT OUTPUT OUTPUT INPUT

  11. Evidence Tracking – Inferred Reactions Direct evidence PMID:5555 PMID:4444 Human pathway Indirect evidence PMID:8976 mouse PMID:1234 cow

  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. Species Selection

  14. Data Expansion – Projecting to Other Species Human B A A + ATP -P + ADP Mouse B A A + ATP + ADP -P Drosophila Reaction not inferred B + ATP A No orthologue - Protein not inferred

  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. Coverage – Current TOC And many more...

  17. Planned Coverage – Editorial Calendar

  18. Reactome Tools Interactive Pathway Browser Pathway Mapping and Over-representation Expression overlay onto pathways Molecular Interaction overlay Biomart

  19. Arabidopsis Reactome http://www.arabidopsisreactome.org/

  20. Tutorial

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

  22. Exercise 1

  23. Search & Analyze bar Zoom/move toolbar Thumbnail Species selector The Pathway Browser Sidebar Pathway Diagram Panel Details Panel (hidden)

  24. Pathways tab – pathway hierarchy Pathway Reaction Black-box

  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. How many sub-pathways does this pathway have? How many reactions are in the first of these sub-pathways? 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. The Pathway Browser - Pathway Diagrams Boxes are proteins, sets or complexes. Ovals are small molecules. Green boxes are proteins or sets, blue are complexes. Regulation +ve -ve Input Reaction node Catalyst Outputs Compartment Transition Binding Dissociation Omitted Uncertain

  27. Exercise 3 From the Homepage, search for the pathway ‘Effects of PIP2 hydrolysis’ and open it in the Pathway Browser. What symbol represents the reaction for ‘Binding of IP3 to the IP3 receptor’? 2. What symbol represents the reaction ‘Transport of Ca++ from platelet dense tubular system to cytoplasm’? What subtype of reaction is this? 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. Navigating in the Pathway Browser I Home and Analyze buttons Search Click here Highlights Details here Click here to open pathway diagram...

  29. Navigating in the Pathway Browser II Highlights Details here Click here Zoom

  30. Exercise 4

  31. The Details Panel

  32. Exercise 5

  33. Pathway Analysis

  34. Pathway Analysis – Overrepresentation ‘Top-level’ Reveal next level P-val

  35. Exercise 6 Check this! What is the most significantly over-represented top-level pathway for this dataset? How many genes are in this pathway, and how many were represented in the dataset? 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) Can you interpret these results in terms of the underlying biology? (Hint: good luck, there are many correct answers!)

  36. Species Comparison I

  37. Species Comparison II Yellow = human/rat Blue = human only Grey = not relevant Black = Complex

  38. Exercise 7

  39. Expression Analysis I

  40. ‘Hot’ = high ‘Cold’ = low Expression Analysis II Step through Data columns

  41. Exercise 8

  42. Molecular Interaction Overlay

  43. Exercise 9 Open the pathway diagram for Netrin-1 Signaling. Find the protein FADK1 (top centre of the cytosol). Right click on it and select Display Interactors. How many are there? How many times has the interaction between FADK1 and Tumor endothelial marker 6 been documented? Hint: This detail is not in Reactome. 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? Display interactors for UNC5B (bottom left of the cytosol). What happens and why? What is the easiest way to remove interactors?

  44. BioMart – selecting your dataset

  45. BioMart – filters

  46. BioMart – attributes Check to get attribute

  47. BioMart – results

  48. Exercise 10

  49. The End

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