June A Database of human biological pathways Steve Jupe - June 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? June Nature Oct 12;407(6805): The biochemistry of apoptosis. Rationale - Figures A picture paints a thousand words but. Just pixels Omits key details Assumes Fact or Hypothesis? June 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 June 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 June human PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Using model organism data to build pathways Inferred pathway events June Theory - Reactions Pathway steps = the units of Reactome = events in biology TRANSPORT CLASSIC BIOCHEMICAL BINDING DISSOCIATION DEGRADATION PHOSPHORYLATION DEPHOSPHORYLATION June Reaction Example 1: Enzymatic June Reaction Example 2: Transport REACT_945.4 Transport of Ca++ from platelet dense tubular system to cytoplasm June Other Reaction Types Binding Dimerization Phosphorylation June Reactions Connect into Pathways OUTPUT INPUT CATALYST OUTPUT INPUT CATALYST INPUT OUTPUT CATALYST June Human pathway PMID:5555PMID:4444 mouse cow Direct evidence Indirect evidence PMID:8976 PMID:1234 Evidence Tracking Inferred Reactions June 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 June Species Selection June 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 June 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 June Coverage Content, TOC And many more... June Planned Coverage Editorial Calendar June Reactome Tools Interactive Pathway Browser Pathway Mapping and Over-representation Expression overlay onto pathways Molecular Interaction overlay Biomart June Tutorial June Front PageSidebar Main text Navigation bar June Exercise 1 June The Pathway Browser Species selector Diagram Key Sidebar Pathway Diagram Panel Details Panel (hidden) Zoom/move toolbar Thumbnail June Pathways tab pathway hierarchy Pathway Reaction Black-box June 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 its not visible, open the Details pane at the bottom of the page by clicking on the blue triangle. June 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 June Exercise 3 June Navigating in the Pathway Browser I Click here Highlights Details here Click here to open pathway diagram... Home and Analyze buttons June Details here Navigating in the Pathway Browser II Click hereZoomHighlights June Exercise 4 June The Details Panel June Exercise 5 June Pathway Analysis June Pathway Analysis Overrepresentation Top-level Reveal next level P-val June 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!) June Species Comparison I June Species Comparison II Yellow = human/rat Blue = human only Grey = not relevant Black = Complex June Exercise 7 June Expression Analysis I June Expression Analysis II Hot = high Cold = low Step through Data columns June Exercise 8 June Molecular Interaction Overlay June Exercise 9 June BioMart selecting your dataset June BioMart filters June BioMart attributes Check to get attribute June BioMart results June Exercise 10 June The End