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A Database of
human biological
pathways
Steve Jupe - [email protected]
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July 2011
www.reactome.org
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 non-human
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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2011
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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
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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
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
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Front Page
http://www.reactome.org
Sidebar
Navigation bar
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Main
text
www.reactome.org
Exercise 1
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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
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 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
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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
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The Details Panel
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Exercise 5
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Pathway Analysis
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Pathway Analysis – Overrepresentation
P-val
Reveal next level
‘Top-level’
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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!)
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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
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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
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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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The End
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