A Database of
human biological
pathways
Steve Jupe - sjupe@ebi.ac.uk
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www.reactome.org
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.
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ELLS 2011
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
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ELLS 2011
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).
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•
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.
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ELLS 2011
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 membranebound 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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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.
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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
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Reactome is…
Extensively cross-referenced
Tools for data analysis –
Pathway Analysis,
Expression Overlay, Species
Comparison, Biomart…
Used to infer orthologous
events in 20 other species
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Using model organism data to build
pathways – Inferred pathway events
PMID:5555
Direct evidence PMID:4444
Direct evidence
human
PMID:8976
mouse
Indirect evidence
PMID:1234
cow
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Theory - Reactions
Pathway steps = the “units” of Reactome
= events in biology
BINDING
DEGRADATION
DISSOCIATION
DEPHOSPHORYLATION
PHOSPHORYLATION
CLASSIC
TRANSPORT
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BIOCHEMICAL
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Reaction Example 1: Enzymatic
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Reaction Example 2: Transport
Transport of Ca++ from platelet dense tubular system to cytoplasm
REACT_945.4
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Other Reaction Types
Dimerization
Binding
Phosphorylation
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Reactions Connect into Pathways
CATALYST
CATALYST
CATALYST
INPUT
OUTPUT
INPUT
OUTPUT
INPUT
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OUTPUT
Evidence Tracking – Inferred Reactions
Direct evidence
PMID:5555
PMID:4444
Human pathway
PMID:8976
Indirect evidence
mouse
PMID:1234
cow
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Species Selection
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Data Expansion – Projecting to Other Species
Human
B
A
+ ATP
A -P + ADP
Mouse
B
A
A -P + ADP
+ ATP
Drosophila
A
+ ATP
B
No orthologue - Protein not inferred
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Reaction not
inferred
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.org
Sidebar
Navigation bar
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Main
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Exercise 1
…see the Tutorial handouts
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The Pathway Browser
Species selector
Diagram Key
Sidebar
Zoom/move
toolbar
Pathway Diagram Panel
Details Panel (hidden)
Thumbnail
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Pathways tab – pathway hierarchy
Pathway
Reaction
Black-box
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Exercise 2
…see the Tutorial handouts
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.
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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
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Binding Dissociation Omitted
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Uncertain
Exercise 3
…see the Tutorial handouts
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Navigating in the Pathway Browser I
Home and Analyze buttons
Click here
Highlights
Details here
Click here to open pathway diagram...
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Navigating in the Pathway Browser II
Click here
Highlights
Zoom
Details here
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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
P-val
Reveal next level
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‘Top-level’
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Exercise 6
…see the Tutorial handouts
Check this!
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Species Comparison I
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Species Comparison II
Yellow = human/rat
Blue = human only
Grey = not relevant
Black = 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
Step through
Data columns
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‘Hot’ = high
‘Cold’ = low
Exercise 8
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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
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BioMart – filters
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BioMart – attributes
Check to get
attribute
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BioMart – results
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Exercise 10
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