A Database of human biological pathways Thawfeek Varusai Please acknowledge Reactome and the sources of Reactome funding (in the panel bottom right). The development of Reactome is supported by grants from the US National Institutes of Health, Ontario Research Fund and the European Molecular Biology Laboratory.

Exercise 1 This exercise helps you to find information via the menu bar and search Is SOX4 in Reactome? How many reactions involve this protein? Is SOX2 in Reactome? How many reactions involve this protein? Is Crb2 in Reactome? Is PI15 in Reactome? Answers are in the tutorial document. This exercise is to gain familiarity with the layout of the homepage and investigate some of the menu items.

Exercise 2 This exercise helps you to understand the organisation of the ‘Hierarchy Panel’. You don’t need to look at the ‘Diagram Panel’. From the ‘Home Page’, search for ‘Signaling by Interleukins’ and click it Under the Locations section, expand the hierarchy by clicking the + button. Select the right level. Avoiding the Diagram Panel on the left: How many sub-pathways are there? How many reactions are in ‘Interleukin-10 signaling’ sub-pathway? What reaction(s) precede and follow ‘IL10 dimer binds IL10RA:JAK1’ event? (Hint: Use the details panel on the bottom right.) Please don’t close this window. You’ll need it for the next exercise. This exercise is to examine the pathway hierarchy on the left.

Exercise 3 This exercise is to help you understand reaction node subtypes. From the previous exercise, expand the ‘Interleukin-10 signaling’ sub-pathway in the hierarchy panel: In the diagram, what symbol represents the reaction node of ‘STAT3 is phosphorylated by p-Y-JAK1,P-Y-TYK2’? What is the node like of the preceding reaction? What is the reaction node like of ‘Expression of PTGS2’? This exercise is to look at the objects on the pathway diagram

Exercise 4 This exercise is to help you understand sub-pathway icons and the relationship between Pathway Hierarchy and Pathway Diagram. Click on the ‘Signaling by Interleukins’ pathway and expand the hierarchy. Observe what happens when you hover the mouse over the different sub-pathways. What happens when you click a sub-pathway? What happens when you click a reaction within a sub- pathway? What happens when you click on a sub-pathway that you’ve already visited? (Reactome Remembers!) Exercise to further establish the connectivity between pathway hierarchy, pathway diagram and details panel.

Exercise 5 This exercise helps you to understand the ‘Details Panel’. Expand ‘Interleukin-7 signaling’ in the hierarchy panel and click ‘JAK3 in IL7:p-Y449-IL7R:JAK1:IL2RG:JAK3 is phosphorylated’. From the details panel: In which cellular compartment(s) does this reaction take place in? What is the GO molecular function associated with the catalyst? Where is the reference paper citing the experimental validation of this reaction? Is this reaction predicted to occur in M. musculus? In C. elegans? Is this event likely to occur in ‘skeletal muscle tissue’? Are there 3D structures available for the proteins involved? Exercise to look at the Details Panel

Exercise 6 This exercise helps you to get an overview of the disease information in Reactome. Go to ‘Signaling by FGFR1 in disease’ from the Reactome homepage or from the Pathway Browser. What disease(s) is/are associated with this pathway? (Hint: look at the Description tab in the Details section). What is the first reaction in this pathway? What is the defective component in the event? How is the defect caused? How many mutations are represented for the defective component? Exercise to look at the Details Panel

Exercise 7 How many hits do you get for the input IDs and how many input IDs were not found? How does the number from question 1 change when ‘Include interactors’ is selected? Which is the most over-represented pathway in this dataset? What proportion of molecules in the top pathway are matched? What proportion of reactions of this pathway are matched?

Exercise 8 From the Reactome homepage, click ‘Analyze Data’ and select the ‘Microarray data’ example set in the right. Click ‘Continue’ and ‘Analyze’. How many hit do you get and how many IDs are not in Reactome? What is the top pathway in the analysis? Select this to reach the diagram. What proportion of the entities in this pathway matches the input data? Can you spot the missing entities from the diagram?

Exercise 9 This exercise is to examine species comparison.

Exercise 10 This exercise is to check that you can use and interpret Molecular Interaction Overlays Open the Pathway Diagram for Netrin-1 Signaling. Find the protein NEO1 (top left of the diagram). How many interactors does it have? What is the confidence score for the interaction between NEO1 and HFE2? How many times has this interaction been documented? Hint: this detail is not in Reactome. Find the protein PTPN11 (below and to the right of NEO1). How many interactors does it have? Can you display just the top 5 interactors based on the confidence score? How do you list all of them?