Introduction to IntAct
Pablo Porras Millán, IntAct
pporras@ebi.ac.uk
Session outline
•
•
Introduction to protein-protein interactions (PPIs)

What are PPIs?

Representing PPIs

PPI databases
IntAct: the molecular interactions database at the EBI

Data structure and curation model

Using the IntAct website
Introduction to protein-protein
interactions (PPIs)
A definition…
Protein-protein interactions (PPIs): physical and selective contacts
that happen between pairs of proteins, in certain molecular regions and
in a defined biological context.
Interactome: the totality of PPIs that happen in a cell / in an organism /
in a specific biological context...
EMBL-EBI
Proteasome image from Hook, B. and Schagat, T. [Internet] 2011. Available from:
www.promega.com/resources/articles/pubhub/functional-proteomics-techniques-to-isolate-and-characterize-the-human-proteasome/
Why protein-protein interactions?
Gene level
DNA
Protein level
RNA
1 protein
=
1 protein
n
=
functions
1 function
=
n
networks!
WRONG!
1. To predict a protein biological function
• “guilt by association”
• proteins with similar functions should cluster together
2. To improve characterization of protein complexes and pathways
• interaction networks work as a draft map that brings detail to
biological processes and pathways
EMBL-EBI
Protein-protein interaction detection methods
Lowthroughput
High-throughput
Yeast-two hybrid (Y2H)
Tandem affinity purification+
mass spectrometry (TAP-MS)
No single method can accurately reproduce a true
binary interaction observed under physiological
conditions – every interaction detected
experimentally is fundamentally artefactual.
X-ray diffraction studies
EMBL-EBI
Representing PPIs: interaction domains
interaction domains
Overlap in sequence ranges:
EMBL-EBI
Representing PPIs:
The problem with complexes
•
Some experimental methods generate complex data: E. g.
Tandem affinity purification (TAP)
•
There are two algorithms to transform this information into
binary data:
EMBL-EBI
Interactions databases: types
De Las Rivas & Fontanillo, PLoS Computational biology, PMID: 20589078.
EMBL-EBI
Primary databases: coverage and biases
Human PPIs coverage in the main
public primary databases
(Dec 2009)
Popularity bias in publicly available
databases
(2013)
Roland et al., Cell, PMID: 25416956.
De Las Rivas & Fontanillo, PLoS Computational biology, PMID: 20589078.
EMBL-EBI
A standard for PPIs representation:
the IMEx consortium
www.imexconsortium.org
Orchard et al., Nature Methods, PMID: 22453911.
EMBL-EBI
IntAct:
The molecular interactions database
at the EBI
IntAct goals & achievements
1. Publicly available repository of molecular interactions (mainly
PPIs) - >530K binary interaction evidences taken from >13,800
publications (September 2015)
2. Data is standards-compliant and available via our website, for
download at our ftp site or via PSICQUIC
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 versions of the software to allow installation
of local IntAct nodes.
EMBL-EBI
IntAct:
Data storage schema
Entry
[A] Publication level (entry)
Publication
Experiment 1
Experiment 2
[B] Experiment level
[C] Interaction level
Interaction 1
Interaction 2
…
[D] Participant level
[E] Feature level
Participant 1
Participant 2
Features
Features
Interaction 3
Interaction 4
…
…
EMBL-EBI
IntAct: PSI-MI ontology
EMBL-EBI
IntAct Curation pipeline
“Lifecycle of an
Interaction”
Sanity Checks
(nightly)
reject
Public web site
Publication
(full text)
.
accept
p2
I
p1
Curation
manual
report
exp
FTP site
check
CVs
annotate
IMEx
report
MatrixDB
curator
Mint
DIP
Super curator
EMBL-EBI
IntAct: the role of the curator
DIRECT SUBMISSION
LARGE DATASETS FROM
HIGH-THROUGHPUT PROJECTS
Gene Ontology
FUNCTION
UniProtKB
PROTEIN
SEQUENCES
PUBLISHED MOLECULAR
INTERACTIONS DATA
CROSS-REFERENCES
ChEBI
SMALL MOLECULES
CURATION
Ensembl
GENOME
SEQUENCES
InterPro
FAMILIES AND
DOMAINS
Others
STRUCTURES,
ORGANISM,
TISSUE...
EMBL-EBI
UniProt Knowledge Base
Interactions can
be mapped to
the canonical
sequence…
... to splice variants...
... or to postprocessed chains
www.uniprot.org
EMBL-EBI
IntAct as a common curation platform
General
curation,
domain int.
General
curation,
large scale
UniProt
entry
related
Extracellular
matrix
Model
organisms
Immune
system
Commercial
curation
Cellular
mechanics
Regulatory
interactions
Specific curation focus/expertise
Host – pathogen
interactions
Cardiovascular
proteins
Other DBs
Common curation platform
Specific Data Dissemination Platforms
EMBL-EBI
www.ebi.ac.uk/intact
IntAct – Home Page
EMBL-EBI
IntAct webpage-based search
EMBL-EBI
IntAct webpage-based search
Details of
interaction
Link to external resource
(UniProtKB)
Details about controlled
vocabulary term describing
interaction detection method
EMBL-EBI
IntAct: changing the layout
EMBL-EBI
IntAct: download formats
EMBL-EBI
PSIMITAB Columns
MITAB 2.5 Standard columns
(15):
ID(s) interactor A & B
• Alt. ID(s) interactor A & B
• Alias(es) interactor A & B
• Interaction detection method(s)
• Publication 1st author(s)
• Publication Identifier(s)
• Taxid interactor A & B
• Interaction type(s)
• Source database(s)
• Interaction identifier(s)
• Confidence value(s)
•
MITAB 2.7 specific columns (+27):
• Expansion method(s)
• Biological role(s) of interactors
• Experimental role(s) of interactors
• Type(s) of interactors
• Properties (CrossReference) of interactors /
interaction
• Annotation(s) of interactors / interaction
• HostOrganism(s)
• Parameters of interaction
• Creation and update dates
• Checksum(s) of interactors / interaction
• Negative
• Feature(s) interactors
• Stoichiometry(s) interactors
• Participant(s) identification method(s)
EMBL-EBI
Interaction detail in IntAct
EMBL-EBI
Interaction detail in IntAct
EMBL-EBI
Interaction detail in IntAct
EMBL-EBI
Interaction detail in IntAct
EMBL-EBI
Filtering results
EMBL-EBI
IntAct: visualizing results as a network
EMBL-EBI
IntAct: visualizing results as a network
EMBL-EBI
IntAct: browse menu
EMBL-EBI
IntAct: Other searches
EMBL-EBI
IntAct: Advanced search
EMBL-EBI
IntAct: Advanced search
EMBL-EBI
IntAct: Advanced search
...
EMBL-EBI
IntAct: MIQL syntax search
EMBL-EBI
More about IntAct: on-line EBI courses
www.ebi.ac.uk/training/online/course/intact-molecular-interactions-ebi
EMBL-EBI
Acknowledgements
MI Team leader
Developing team
Sandra
Orchard
Max Koch
Curation team
Margaret
Duesbury
Birgit
Meldal
Mariaestela
Ortiz
EMBL-EBI