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www.reactome.org March 20131
A Database of human
biological pathways
Steve Jupe - sjupe@ebi.ac.uk
www.reactome.org March 20132
Background
• Cells contain thousands of molecules, – proteins and small chemical compounds
• They work together to perform tasks. – provide energy
– produce materials
– respond to the environment.
• Processes require coordinated efforts– like a factory production line.
– Biologists refer to a chain of connected molecular events as a pathway.
ELLS 2011
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Different types of pathways
• Metabolic networks – provide the energy and materials
• Signaling networks – sense the outside, coordinate activities within and between cells
• (Gene) regulatory networks – control processes, set limits, control the molecular composition of cells
ELLS 2011
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The scale of pathways
• Early pathways were pieced together by studying biochemical reactions of individual proteins, measuring the activity, learning the substrates and products, joining them to the next enzyme in the pathway.
• New technologies allow simultaneous measurement of tens of thousands of different molecules.
• This reveals that many biological pathways are interconnected, more complicated than the typical textbook examples, with fluid boundaries. They can work together or against each other (feedback and regulation).
• Scientists who study or interpret these large scale interactions sometimes refer to the field as ‘systems biology’
• When multiple biological pathways interact = a biological network.
• When all possible interactions are added, pathways become extremely difficult to understand
• Biologists often work with ‘canonical’ pathways, those that represent the well-understood part of the entire network.
ELLS 2011
www.reactome.org March 20135
Rationale – Journal informationNature 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?
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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?
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Reactome is…
Free, online, open-source curateddatabase of pathways and reactions in human biology
Authored by expert biologists, maintained by Reactome editorial staff (curators)
Mapped to cellular compartment
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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…
www.reactome.org March 20139
human
PMID:5555 PMID:4444
mouse
cow
Direct evidence
Direct evidence
Indirect evidence
PMID:8976
PMID:1234
Using model organism data to build pathways – Inferred pathway events
www.reactome.org March 201310
Theory - Reactions
Pathway steps = the “units” of Reactome
= events in biology
TRANSPORTCLASSIC
BIOCHEMICAL
BINDING
DISSOCIATION
DEGRADATION
PHOSPHORYLATION
DEPHOSPHORYLATION
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Reaction Example 1: Enzymatic
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Reaction Example 2: Transport
REACT_945.4
Transport of Ca++ from platelet dense tubular system to cytoplasm
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Other Reaction Types
Binding
Dimerization
Phosphorylation
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Reactions Connect into Pathways
OUTPUTINPUT
CATALYST
OUTPUTINPUT
CATALYST
INPUT OUTPUT
CATALYST
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Human pathway
PMID:5555 PMID:4444
mouse
cow
Direct evidence
Indirect evidencePMID:8976
PMID:1234
Evidence Tracking – Inferred Reactions
www.reactome.org March 201316
Species Selection
www.reactome.org March 201317
Data Expansion – Projecting to Other Species
A + ATP A + ADP-PB
Human
A + ATP A + ADP-P
BMouse
BA
Drosophila
Reaction notinferred
No orthologue - Protein not inferred
+ ATP
www.reactome.org March 201318
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
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Coverage – Content, TOC
And many more...
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Planned Coverage – Editorial Calendar
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Reactome Tools
• Interactive Pathway Browser
• Pathway Mapping and Over-representation
• Expression overlay onto pathways
• Molecular Interaction overlay
• Biomart
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Tutorial
Tutorial handouts in your info packages…
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Front Page http://www.reactome.orgS
ide
bar Main
text
Navigation bar
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Exercise 1
…see the Tutorial handouts
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The Pathway BrowserSpecies selector
Diagram Key
Sidebar
Pathway Diagram Panel
Details Panel (hidden)
Zoom/move toolbar
Thumbnail
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Pathways tab – pathway hierarchy
PathwayReactionBlack-box
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Exercise 2
From the homepage, search for ‘PDGF 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 Processing of classical PDGFs?Hint: If it’s not visible, open the Details pane at the bottom of the
page by clicking on the blue triangle.
…see the Tutorial handouts
www.reactome.org March 201328
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
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Exercise 3
…see the Tutorial handouts
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Navigating in the Pathway Browser I
Click here
Highlights
Details here
Click here to open pathway diagram...
Home and Analyze buttons
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Details here
Navigating in the Pathway Browser II
Click here
ZoomHighlights
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Exercise 4
…see the Tutorial handouts
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The Details Panel
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Exercise 5
…see the Tutorial handouts
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Pathway Analysis
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Pathway Analysis – Overrepresentation
‘Top-level’
Reveal next level
P-val
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Exercise 6
Check this!
…see the Tutorial handouts
www.reactome.org March 201338
Species Comparison I
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Species Comparison II
Yellow = human/rat Blue = human onlyGrey = not relevantBlack = Complex
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Exercise 7
…see the Tutorial handouts
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Expression Analysis I
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Expression Analysis II ‘Hot’ = high‘Cold’ = low
Step throughData columns
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Exercise 8
www.reactome.org March 201344
Molecular Interaction Overlay
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Exercise 9
…see the Tutorial handouts
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New Look Browser
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End
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BioMart – selecting your dataset
www.reactome.org March 201349
BioMart – filters
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BioMart – attributes
Check to get
attribute
www.reactome.org March 201351
BioMart – results
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Exercise 10
Recommended