Transcript Presentation

Exploring Interactions & Pathways
Pablo Porras Millán,
IntAct
Session outline
1. An example of an interaction database: IntAct hands-on.
2. A manually-curated pathway database: Reactome hands-on.
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IntAct:
The molecular interactions database
at the EBI
www.ebi.ac.uk/intact
IntAct – Home Page
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IntAct webpage-based search
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IntAct webpage-based search
Details of
interaction
Choice of UniProtKB
or Dasty View
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IntAct: changing the layout
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IntAct: download formats
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Interaction detail in IntAct
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Detailed participant information:
Dasty view
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IntAct: filtering results
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IntAct: visualizing results
as a network
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IntAct: using lists
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IntAct: browse menu
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IntAct: advanced search
...
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IntAct: MIQL syntax search
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Reactome tutorial
Reactome Tools
• Interactive Pathway Browser
• Pathway Mapping and Over-representation
• Expression overlay onto pathways
• Molecular Interaction overlay
• Biomart
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Front Page
http://www.reactome.org
Sidebar
Navigation bar
Main
text
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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 Binding Dissociation Omitted
Uncertain
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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
Zoom
Highlights
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
1. Find the reaction ‘Activated type I receptor phosphorylates SMAD2/3
directly’. What pathway does it belong to?
2. In which cellular compartment does this reaction take place?
3. What is the associated GO molecular function?
4. What references verify this reaction?
5. Is this reaction predicted to occur in Canis familiaris? In
Saccharomyces cerevisiae?
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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
Use data file from earlier
exercises…
Copy, and paste into submissions
box…
Check this!
1. What is the top ‘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 ‘Signal transduction’ higher in the list
than ‘DNA repair’, when the latter has a more significant probability
score? (Hint - use the Open All button)
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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
Launch Species Comparison and select the species Rattus
norvegicus. When the results are displayed, open the pathway
‘Membrane trafficking’.
1. Find VAMP7 (top right of diagram) - what colour is it and why?
2. Which other species are inferred to have this protein? Hint: You
can answer this question without re-running Species comparison.
3. Find CHMP7 (top middle) - why is it blue?
4. Find AP-1 Complex (top middle, a bit to the right, below CHMP7) Why is it black? How many proteins contribute to this object? Are
they all predicted to exist in Rattus norvegicus?
5. Why is ADP grey?
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Expression Analysis I
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Expression Analysis II
‘Hot’ = high
‘Cold’ = low
Step through
Data columns
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Exercise 8
Launch Expression Analysis and load the example dataset. Click
‘Analyse’. When the results are displayed, find the pathway ‘DNA
replication’.
1. How many proteins are in this pathway?
2. How many had expression data?
Click on the View button to see this pathway in the Pathway Browser
and then go to the ‘Regulation of DNA replication’ subpathway. Use the
Experiment Browser toolbar to cycle through the timepoints.
3. Which protein has the greatest change of expression?
4. Find the complex ‘Orc4:Orc5:Orc3:Orc2:origin’ (top left of the
diagram). Which component of the complex has the lowest
expression at 24h?
5. What was the probe ID used to measure expression of this
component?
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Molecular Interaction Overlay
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Exercise 9
…see the Tutorial handouts
Open the Pathway Diagram for ‘Netrin-1 Signaling’.
1. Find the protein PTPN11 (top left of the plasma membrane). Right
click on it and select Display Interactors. How many are there?
2. How many times has the interaction between PTPN11 and
A7MD36 (UniProtKb for GAB2) been documented? Hint: This
detail is not in Reactome.
3. Find the protein SRC (just to the right of PTPN11). Display
interactors for this protein. How many are there? Can you get a
list of them?
4. What is the easiest way to remove interactors?
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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 Reactome Pathways Portal (Beta)
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Protein structures from PDBe
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Chemical structures from ChEBI
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Expression data from the Expression Atlas
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Interaction Data from IntAct
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More about Reactome
Reactome User's Guide
http://wiki.reactome.org/index.php/Usersguide
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Websites & Tools
• IntAct
– www.ebi.ac.uk/intact
• PSICQUIC view
– www.ebi.ac.uk/Tools/webservices/psicquic/view
• Reactome
– www.reactome.org
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Acknowledgements
Group leader
Supported by the European Community's
Seventh Framework Programme
(FP7/2007-2013) under grant agreement for
Affinomics (FP7-241481).
Henning Hermjakob
Coordinator
Sandra
Orchard
Curation team
Margaret
Duesbury
Birgit
Meldal
Steve Jupe
Antonio
Fabregat
Bijay Jassal
Phani
Garapati
David Croft
Developing team
Rafael
Jiménez
Marine
Dumousseau
Noemí
del Toro
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