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What is this view?

Binary interactions

In this tab, we display the list of interactions that you have selected using one of our search features. Despite the fact that our data are annotated to accurately reflect the interactions reported in scientific literature, the data is shown in this view as binary interactions. Whenever the data was reported as a co-complex involving more than two molecules, we store it as such in the IntAct database and post-process it so the portal can show it as binary interaction. This post-processing is the Spoke Expansion model (connects bait to all preys):



sourceExp

At any moment you can choose to display the expansion column in this view in order to see which interaction are spoke expanded and which are not.

Description of what has changed

  • We have added more download options to allow users to retrieve their interaction set using more standard formats such as PSI-MI XML and PSIMITAB (version 2.5, 2.6 or 2.7) but also XGMML, RDF and Biopax (level 2 and 3).
  • We have now four different table views : minimal(molecule names and interaction AC), basic (minimal + molecule links, interaction detection method, negative), standard(minimal + molecule species, confidences, publication details, experiment details), expanded (standard + more experiment details) and complete (all mitab 2.7 columns).

Configuring the view to your need"

In the header of the interaction table you will find a button: ‘Change Column Display’ that will show you all the columns/Table views available and allow you to update the current selected set.

Downloading the data into Standard formats"

In the header of the interaction table you will find a drop down list that contains all the formats currently supported when downloading the interaction data. Select one of them and click the export button next to the list. Please note that PSI-MI XML is only available when the interaction set is no bigger than 1000 interactions.

Opening the interaction details"

Clicking on the magnifying glass in the first column of the interaction table will open the details of the corresponding interaction in the Interaction Details tab, giving you access to more details of the manually curated record.

What is this view?

Browsing (Browse Tab)

This tab is meant to give you access to more content based on the currently selected set of interactions. Please note that linking to third party resources will only include up to 200 molecules , if you exceed this number you will see the warning icon (This number has been reduced to 125 molecules for mRNA expression). Now let’s look at the features available to you:

Limiting the scope of the current dataset with the Uniprot Taxonomy ontology

Allows users to browse the Uniprot Taxonomy hierarchy as a tree and select terms in order to narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.

Limiting the scope of the current dataset with the GO ontology

Allows users to browse the GO hierarchy as a tree and select terms in order to narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.

Limiting the scope of the current dataset with the ChEBI ontology

Allows users to browse the ChEBI hierarchy as a tree and select terms in order to narrow down their dataset. Once a term is selected, you are taken back to the interaction tab to review your dataset.

Bulk linking to third party resources by using involved proteins

  • Proteins by Reactome pathway: Sends your proteins to the Reactome SkyPainter that will show you the pathways in which these molecules are know to play a role.
  • Proteins by Chromosomal location: Sends your list of proteins to Ensembl’s Karyotype viewer and overlays the proteins on the chromosomes.
  • Proteins by mRNA expression: Sends your set of proteins to the ArrayExpress Atlas that will show the known gene expression based on experimental studies.
What is this view?

Searching Interactions (Search Tab)

As you can see in this tab we are now trying to give you more targeted choice to do your queries, please note that the examples provided in this tab are live links so you can simply click them to see the resulting interactions sets.

Using the Quick Search

In this search panel you are free to type anything that might relate to interactions, whether it is properties of their interactor (gene name, identifiers, GO term…) or more specific to the interaction like publication, authors, experimental detection method, ...

Some examples:

  • Try the query: imatinib
    This is a drug for which we have curated a number of interactions.
    Once you press the search button you should be taken to the Interaction Tab that lists 130 binary interactions.
    If you want to construct more complex queries we recommend you take a look at the Molecular Interaction Query Language, accessible from the quick search panel.
  • Try the query: species:yeast AND type:"direct interaction"
    This query selects all interactions involving yeast interactors that have been shown to have direct interactions. If you customize the column display of the interaction tab, you will see that not only “direct interaction” have been selected but also children terms in the PSI-MI ontology.

Using the Ontology Search

Open the Rearch Tab. This panel is specialised to give you an easy access to ontology search. So far you can search on 4 ontologies:

  • Gene Ontology
  • InterPro
  • PSI-MI
  • ChEBI

Whenever you start typing a query in this search panel, the system will search as you type and propose a list of matching controlled vocabulary terms. You can then select one of them and select matching interactions.

For example, type: cancer
You will be presented with a few choices, please note that each term is followed by the count of matching interactions in the IntAct database.

Select a term with the mouse or using the keyboard cursor keys and you will be taken to the interaction tab.

Searching the Compound chemical structure

In this panel you will be able to draw all or part of a chemical structure and search for chemical compounds. If you get any matched, you can then see all interactions involving them.

First you have to open up the chemical search panel so that the applet can load, it might take a few seconds. Then you can start drawing your structure, for instance:

Once you have drawn your structure, select Similarity and press Search. You should be presented with a list of matching compound. Now choose one molecule and click the link: IntAct interactions. You will be taken to the interaction tab to review the data.

Complex Expansion

Binary interactions generated by co-complex expansion

Why should you care about complex expansion ?

Some experimental methods such as Tandem Affinity Purification do generate molecular interactions that can involve more than 2 molecules. Despite the fact that IntAct curation team do capture the molecular interaction as they were reported in the corresponding experiment, when you search using the intact web site, the results of your query is always shown as set of binary interactions (i.e. 2 molecules). We would like to draw your attention on the fact that whenever the reported interaction was a co-complex we do apply an expansion algorithm that transform this n-ary interaction into a set of binary interactions. While none of these agorithms is perfect and will very likely generate some false positive interactions, it is useful to present the data in a consistent manner. Bear in mind that we will strive to differentiate in the search results which interactions are a real experimental binary from expanded ones.

Existing expansion algorithm

There are several known algorithm allowing to transform an n-ary interaction into a set of binaries. The illustration below present the two well known expansion model and illustrates why they can be incorrect.



sourceExp

  • Spoke expansion: Links the bait molecule to all prey molecules. If N is the count of molecule in the complex, it generated N-1 binary interactions.
  • Matrix expansion: Links all molecule to all other molecule present in the complex. If N is the count of molecule in the complex, it generated (N*(N-1))/2 binary interactions.

Now the issue (as illustrated at the bottom right of the diagram above) with these two models lies in the fact that the real complex might not be articulated around the experimental bait but instead, this bait might be linked to a smaller complex, hence most binary interaction generated by spoke and matrix expansion result in false positive.



PSICQUIC

How is the number of interactions in other databases obtained?

PSICQUIC is a standard way to access molecular interaction databases across which it repeats the same query. The number of databases providing data may vary, depending on the status of their services and only those that are active are used in this query. By clicking on the number of interactions you will be redirected to the PSICQUIC View, where you can browse the results in those other resources.

The services currently active are:

Check the PSICQUIC site for more information.

IMEx

What is the significance of the IMEx dataset?"

IMEx is a network of databases which have agreed to supply a non-redundant set of data expertly manually annotated to the same consistent detailed standard which, as such, represents a high-quality subset of the data each individually provides. The number of databases providing data may vary, depending on the status of their services and only those that are active are used in this query. By clicking on the number of interactions you will be redirected to the IMEx View, where you can browse the results in those other resources.

The services currently active are:

Check the IMEx site for more information.

What is this view?

Representation of Experimental Features

This section shows the graphical representation of experimental features, where each participant is represented as a white rectangle with a black border and a line for each hundredth amino acid. All available features are attached to their associated participant and their categories are represented in the right side of the legend. The left side of the legend dynamically shows the range statuses occuring in the shown interaction. These are the possible range statuses:

sourceExp

Interacting with the widget

Hover over a feature to see more information in a tooltip.
sourceExp

To display a single interacting region click on it and click again to display all interacting regions.
Displaying all interacting regionsDisplaying one interacting region
sourceExpsourceExp
What is this view?

Dynamic molecular interaction data

This section shows the graphical representation of dynamic molecular interactions. By default it displays all the interactions from one experiment using radio buttons to allow users to highlight interactions in different variable conditions.

Publication

PubMed Id: 16497658

Journal: RNA (1355-8382)

Year of Publication: 2006

Title: AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II.

Author List: Gullerova M., Barta A., Lorkovic ZJ.

Cross References:

Database
Identifier
Secondary identifier
Qualifier
-

Experiment (5 interactions)

Accession: EBI-1540478

Name: gullerova-2006-4

Host organism: Nicotiana tabacum (Common tobacco)

Organism: Nicotiana tabacum (Common tobacco)

Accession: EBI-541265

Name: tobac

Description: Nicotiana tabacum (Common tobacco)

Cross References:

Database
Identifier
Secondary identifier
Qualifier
-

Interaction Detection Method: confocal microscopy

Interaction detection method: confocal microscopy
Accession: EBI-933927

Name: confocal microscopy

Description: confocal microscopy

Cross References:
Database
Identifier
Secondary identifier
Qualifier
psi-mi
MI:0663
-
identity
pubmed
14755292
-
primary-reference


Annotations:
Topic
Text
definition
A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen.


Participant Identification Method: predetermined

Participant identification method: predetermined
Accession: EBI-1465

Name: predetermined

Description: predetermined participant

Cross References:
Database
Identifier
Secondary identifier
Qualifier
psi-mi
MI:0396
-
identity
pubmed
14755292
-
primary-reference


Annotations:
Topic
Text
definition
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).


Cross References:

Database
Identifier
Secondary identifier
Qualifier
-

Annotations:

Topic
Text
zdravko.lorkovic@univie.ac.at, andrea.barta@univie.ac.at
Confocal microscopy analysis was carried out on tobacco protoplasts which transiently expressed epitope tagged fusion proteins.
The cDNA library was made from random-primed mRNA, isolated from mature Arabidopsis leaves and roots.

Interaction

Accession: EBI-1540486

Name: cyp59-srp30-1

Description: Colocalisation of cyp59 protein and Srp30 protein

Type: colocalization

Interaction type: colocalization
Accession: EBI-608832

Name: colocalization

Description: colocalization

Cross References:
Database
Identifier
Secondary identifier
Qualifier
psi-mi
MI:0403
-
identity
pubmed
14755292
-
primary-reference


Annotations:
Topic
Text
definition
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.


Cross References:

Database
Identifier
Secondary identifier
Qualifier
nucleus

Annotations:

Topic
Text
6
In cells coexpressing SRp30-RFP and AtCyp59-GFP only low levels of colocalization were observed.
The protein sequence provided for Arabidopsis AtCyp59 in Figure 1 differs from the protein sequence present in the UniProt record. The UniProt record has an insertion of the following amino acid sequence 'DFSQ SVSKLWSQFR QKDSQK' between residues 317 to 336.

Participants (2)

Legend:
A
Annotation and Cross Reference  
P
Experimental Parameter   
S
Stoichiometry   
F
Experimental Feature
C
Participant Confidence
#
Name
Links
Primary Identifier
Aliases
Description
Species
Expression system
Experimental role
Biological role
Interactor type
More...
1
EBI-1540237
 logo
dastyLogo
SR30
SF2/ASF-like splicing modulator Srp30
SRP30

[+3]
Serine/arginine-rich splicing factor SR30
Arabidopsis thaliana (Mouse-ear cress)
Organism Details

Accession: EBI-297767

Name: arath

Description: Arabidopsis thaliana (Mouse-ear cress)

Cross References:

Database
Identifier
Secondary identifier
Qualifier
-
-

Expressed In Details

Accession:

Name:

-
neutral component
Experimental role: neutral component
Accession: EBI-55

Name: neutral component

Description: neutral component

Cross References:
Database
Identifier
Secondary identifier
Qualifier
psi-mi
MI:0497
-
identity
pubmed
14755292
-
primary-reference


Annotations:
Topic
Text
definition
Molecule role in an experimental setting that does not have an embedded asymmetry.


unspecified role
Biological role: unspecified role
Accession: EBI-77781

Name: unspecified role

Description: unspecified role

Cross References:
Database
Identifier
Secondary identifier
Qualifier
psi-mi
MI:0499
-
identity
pubmed
14755292
-
primary-reference


Annotations:
Topic
Text
definition
Role not specified or not applicable to the data.


protein
Interactor type: protein
Accession: EBI-619654

Name: protein

Description: protein

Cross References:
Database
Identifier
Secondary identifier
Qualifier
psi-mi
MI:0326
-
identity
pubmed
14755292
-
primary-reference
so
SO:0000358
-
see-also


Annotations:
Topic
Text
definition
A linear polymer of amino acids joined by peptide bonds in a specific sequence.


A
Participant: Serine/arginine-rich splicing factor SR30

Participant: Serine/arginine-rich splicing factor SR30

Accession: EBI-1540492

Name: EBI-1540237

P
Participant: Serine/arginine-rich splicing factor SR30

Participant: Serine/arginine-rich splicing factor SR30

Accession: EBI-1540492

Name: EBI-1540237

Parameters:

Type
Value
Unit
Base
Exponent
Uncertainty
No records found.


S
Participant: Serine/arginine-rich splicing factor SR30

Participant: Serine/arginine-rich splicing factor SR30

Accession: EBI-1540492

Name: EBI-1540237

Stoichiometry: 0.0

F
Participant: Serine/arginine-rich splicing factor SR30

Participant: Serine/arginine-rich splicing factor SR30

Accession: EBI-1540492

Name: EBI-1540237

Features:

Legend:
A
Annotation and Cross Reference  
Feature Name
Feature Type
Detection Method
Range positions
More...
region
  • ?-?
  • A
    Feature: EBI-1540493

    Feature: region

    Accession: EBI-1540493

    Name: region


    C
    Participant: Serine/arginine-rich splicing factor SR30

    Participant: Serine/arginine-rich splicing factor SR30

    Accession: EBI-1540492

    Name: EBI-1540237

    Confidences:

    Type
    Value
    No records found.

    2
    EBI-1625989
     logo
    dastyLogo
    CYP59
    Cyclophilin-59
    F22G10.24

    [+1]
    Peptidyl-prolyl cis-trans isomerase CYP59
    Arabidopsis thaliana (Mouse-ear cress)
    Organism Details

    Accession: EBI-297767

    Name: arath

    Description: Arabidopsis thaliana (Mouse-ear cress)

    Cross References:

    Database
    Identifier
    Secondary identifier
    Qualifier
    -
    -

    Expressed In Details

    Accession:

    Name:

    -
    neutral component
    Experimental role: neutral component
    Accession: EBI-55

    Name: neutral component

    Description: neutral component

    Cross References:
    Database
    Identifier
    Secondary identifier
    Qualifier
    psi-mi
    MI:0497
    -
    identity
    pubmed
    14755292
    -
    primary-reference


    Annotations:
    Topic
    Text
    definition
    Molecule role in an experimental setting that does not have an embedded asymmetry.


    unspecified role
    Biological role: unspecified role
    Accession: EBI-77781

    Name: unspecified role

    Description: unspecified role

    Cross References:
    Database
    Identifier
    Secondary identifier
    Qualifier
    psi-mi
    MI:0499
    -
    identity
    pubmed
    14755292
    -
    primary-reference


    Annotations:
    Topic
    Text
    definition
    Role not specified or not applicable to the data.


    protein
    Interactor type: protein
    Accession: EBI-619654

    Name: protein

    Description: protein

    Cross References:
    Database
    Identifier
    Secondary identifier
    Qualifier
    psi-mi
    MI:0326
    -
    identity
    pubmed
    14755292
    -
    primary-reference
    so
    SO:0000358
    -
    see-also


    Annotations:
    Topic
    Text
    definition
    A linear polymer of amino acids joined by peptide bonds in a specific sequence.


    A
    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Accession: EBI-1632638

    Name: EBI-1625989

    P
    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Accession: EBI-1632638

    Name: EBI-1625989

    Parameters:

    Type
    Value
    Unit
    Base
    Exponent
    Uncertainty
    No records found.


    S
    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Accession: EBI-1632638

    Name: EBI-1625989

    Stoichiometry: 0.0

    F
    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Accession: EBI-1632638

    Name: EBI-1625989

    Features:

    Legend:
    A
    Annotation and Cross Reference  
    Feature Name
    Feature Type
    Detection Method
    Range positions
    More...
    region
  • ?-?
  • A
    Feature: EBI-1632639

    Feature: region

    Accession: EBI-1632639

    Name: region


    C
    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Participant: Peptidyl-prolyl cis-trans isomerase CYP59

    Accession: EBI-1632638

    Name: EBI-1625989

    Confidences:

    Type
    Value
    No records found.


    Graphical Representation of Experimental Features