A Database of human biological pathways Steve Jupe - email@example.com
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?
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.
Reactome is… Free, online, open-source curated database of pathways and reactions in human biology Authored by expert biologists, maintained by Reactomeeditorial staff (curators) Mapped to cellular compartment
Reactome is… Extensively cross-referenced Toolsfor data analysis – Pathway Analysis, Expression Overlay, Species Comparison, Biomart… Used to infer orthologous events in 20 other species
Using model organism data to build pathways – Inferred pathway events Direct evidence PMID:5555 PMID:4444 Direct evidence human PMID:8976 mouse Indirect evidence PMID:1234 cow
BINDING DEGRADATION DISSOCIATION DEPHOSPHORYLATION PHOSPHORYLATION CLASSIC BIOCHEMICAL TRANSPORT Theory - Reactions Pathway steps = the “units” of Reactome = events in biology
Reaction Example 2: Transport Transport of Ca++ from platelet dense tubular system to cytoplasm REACT_945.4
Other Reaction Types Dimerization Binding Phosphorylation
Reactions Connect into Pathways CATALYST CATALYST CATALYST INPUT OUTPUT INPUT OUTPUT OUTPUT INPUT
Evidence Tracking – Inferred Reactions Direct evidence PMID:5555 PMID:4444 Human pathway Indirect evidence PMID:8976 mouse PMID:1234 cow
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
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
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
Coverage – Content, TOC And many more...
Reactome Tools • Interactive Pathway Browser • Pathway Mapping and Over-representation • Expression overlay onto pathways • Molecular Interaction overlay • Biomart
Front Page http://www.reactome.org Navigation bar Sidebar Main text
Zoom/move toolbar Thumbnail Species selector The Pathway Browser Diagram Key Sidebar Pathway Diagram Panel Details Panel (hidden)
Pathways tab – pathway hierarchy Pathway Reaction Black-box
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.
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. Regulation +ve -ve Input Reaction node Catalyst Outputs Compartment Transition Binding Dissociation Omitted Uncertain
Navigating in the Pathway Browser I Home and Analyze buttons Click here Highlights Details here Click here to open pathway diagram...
Navigating in the Pathway Browser II Highlights Details here Click here Zoom
Pathway Analysis – Overrepresentation ‘Top-level’ Reveal next level P-val
Exercise 6 Check this!
Species Comparison II Yellow = human/rat Blue = human only Grey = not relevant Black = Complex
‘Hot’ = high ‘Cold’ = low Expression Analysis II Step through Data columns
BioMart – attributes Check to get attribute