The IntAct Database
Sandra Orchard & Birgit Meldal
IntAct goals & achievements
1. Publicly available repository of molecular
interactions (mainly PPIs) - >333K binary
interactions taken from >6620 publications (Aug
2013)
2. Data is standards-compliant and available via our
website, for download at our ftp site or via PSICQUIC
http://www.ebi.ac.uk/intact
ftp://ftp.ebi.ac.uk/pub/databases/intact
www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml
3. Provide open-access editor for those who wish to
curate molecular interactions.
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IntAct Curation
“Lifecycle of an Interaction”
Sanity Checks
(nightly)
reject
Public web site
Publication
(full text)
.
exp
accept
p2
I
p1
FTP site
check
CVs
annotate
Curation
manual
IMEx
report
report
MatrixDB
curator
Master headline
Super curator
Mint
DIP
UniProt Knowledge Base
http://www.ebi.uniprot.org/
Interactions can
be mapped to
the canonical
sequence…
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.. to splice variants..
.. or to postprocessed chains
Relationship with UniProtKB
Interaction
curation
Protein
sequence
Data filters
High confidence
PPIs
Other
DBs
Master headline
Other IMEx
databases
Data model
•
Support for detailed features
i.e. definition of interacting interface
Interacting domains
Overlay of Ranges on sequence:
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How to deal with Complexes
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•
Some experimental protocol do generate complex data:
Eg. Tandem affinity purification (TAP)
•
One may want to convert these complexes into sets of
binary interactions, 2 algorithms are available:
Performing and visualing a Simple
Search
http://www.ebi.ac.uk/intact
IntAct – Home Page
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Performing a Simple Search
1
From search to networkView…
Visualizing - networkView
1
Extend and Visualise your Search
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Visualisation – network view
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Cytoscape Web
• Cytoscape Web - web-based network visualization tool
• Modeled after Cytoscape – open-source, interactive,
customizable and easily integrated into web sites.
• Contains none of the plugin architecture functionality of
Cytoscape
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Opening the network in Cytoscape…
Visualisation
Master headline
Applying a better graph layout…
Visualization
Master headline
Applying a better graph layout…
Visualization
Master headline
Highlighting network properties…
Visualization
Master headline
Highlighting network properties…
Visualization
Master headline
Highlighting network properties…
Visualization
Master headline
Highlighting network properties…
Visualization
Master headline
Cytoscape Plugins
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Exploring a single interaction in more
depth
Interaction detail
Details of
interaction
2
Choice of UniProtKB
or Dasty View
UniProt
PubMed/IMEx ID
Detail of interaction
Details of
interaction
2
Interaction
Score
Expansion
method
Interaction Score
• All evidences of Protein A interacting with Protein B are
clustered.
• Evidences are scored according to
a. Interaction detection method
b. Interaction type
c. Number of publications interaction has been observed in
Score is normalised on 0-1 scale
Low score – low confidence interaction
High score – high confidence interaction
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Search result for ‘RAD1’
Participant information
2
Binary view of o60671_human
Browsing – Molecule View
2
First search from the home page…
Interaction detail
2
Details of
interaction
Viewing Interaction Details
Additional
information
3
Interaction Details
3
IntAct – Home Page-Quick Search
3
Advanced search
Filtering options
Add more filtering options
Ontology search
3
First search from the home page…
Searching with MIQL
3
•
Using the Molecular Interaction Query Language
(MIQL), one can also build complex queries
•
List of terms one can query on :
Network analysis
Analyzing protein-protein interaction networks.
Koh GC , Porras P , Aranda B , Hermjakob H , Orchard SE
PMID:22385417
J Proteome Res [2012 (11) ] page info:2014-31
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www.ebi.ac.uk/training/online
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