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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):


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.


  • 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.


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.


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:


Interacting with the widget

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

To display a single interacting region click on it and click again to display all interacting regions.
Displaying all interacting regionsDisplaying one interacting region
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.


I have found no interactions for my protein rat Zap70. How do I find if a homolog/ortholog/paralog with a high degree of sequence similarity has any interactions in the IntAct database?

Go to
Select your Search Engine of choice e.g. NCBI-BLAST

Click on protein then paste your sequence into the box, make any required changes to the parameters, add your e-mail address and Submit.

You will receive the results in tabular form, with additional hyperlinks through to other databases containing information about this protein.
You can see below that, although InAct contains no molecular interactions for rat or mouse it does for human

Press on the link to access the data in IntAct

How to link to the IntAct website?

There are currently 5 supported ways to link to the IntAct website:

  1. Interaction tab using a free text query (MIQL):
  2. Details tab by experiment AC:
    Given an experiment AC, one can open the details view.
    Note: this will not show any interaction details but only experiment and respective publication.
  3. Details tab by interaction AC:
    Given an interaction AC, one can open the detail view, for instance:
  4. Interaction given a pair of interactor:
    Given two interactors' AC, one can open the interaction detail view, for instance:
  5. Molecule view by interactor AC:
    Given an interactor AC, one can open the Molecule view (Dasty2), for instance:


Why does the number of interactions given in a particular high-throughput paper, differ from the number I can download from IntAct from the same publication?

Authors state the number of interactions they have identified, based on protein sequence identifications made at the time of going to press. When we upload this data into the IntAct molecular interaction database, we map these identifications to the UniProtKB protein sequence database, so that our users can benefit from the high-quality manual annotation of these sequences performed by the UniProtKB/Swiss-Prot curators. The number of interactions can vary both as a result of this process and also as a result of time for the following reasons.

  • The author may have used a redundant database to identify their proteins. We often find separate identifiers map to a common non-redundant UniProtKB entry and an interaction turns out to have been identified twice, but originally assigned to different protein IDs.
  • Proteins may have been withdrawn from the protein sequence database over time - this is particularity true for predicted proteins based on gene models. If we cannot remap the protein to an appropriate alternative, we may have to withdraw the interaction.
  • Gene models may merge resulting in only one interacting pair being identified, where previously there was thought to be two.
  • Gene models may be split over time - in this case any interaction based on a protein product of the original gene model will have to be withdrawn unless we have enough data to tell us which of the new proteins is involved in the interaction.
  • Authors may submit additional interactions which they did not describe in the original paper but were generated by the same method. This will be maintained separately and labelled as such.
  • Some interactions pairs included by the author may break the annotation rules of both the IntAct molecular interaction database and the IMEx consortium If so, these interactions are excluded and a note added as a "data-processing" comment to explain why.

Data export

How are binary interactions selected for export to UniProtKB/GOA records?

All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non- redundant set of protein pairs. Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair. Only experimental data is scored, inferred interactions, for example, would not be scored, and any low confidence data, or data manually tagged by a curator for exclusion from the process, are also not scored. Isoforms and post-processed protein chains are regarded as individual proteins for scoring purposes. We will, in future, export negative information, particularly for isoforms when one isoform of a protein behaves differently from another.

Score weightings were determined using the PSI-MI CV (available here) hierarchy i.e

Interaction Detection Method Weighting
Biochemical 3
Biophysical 3
Protein complementation Assay (PCA) 2
Imaging Techniques 0.6

Interaction Type Weighting
Association 1
Physical Association 2
Direct Association (and child terms) 5
Colocalization 0.2

Example 1 :

Protein A - Protein B – the interaction has been shown by one yeast two-hybrid experiment and one coimmunoprecipitation as part of an affinity complex from a cellular environment.
1xY2H (PCA) + Physical interaction = 2+2 =4
1x coimmunopreciptiation + Association = 3+1 =4
Total score = 8

Example 2 :

Protein C - Protein D – the interaction has been shown by two yeast two-hybrid experiment, by one GST pulldown in vitro and by one X-ray crystal.
2xY2H (PCA) + Physical interaction = 2(2+2) =8
1x pulldown + direct interaction = 3+5 =8
1x x-ray crystal + direct interaction = 8
Total score = 24

Once the interactions have been scored, a cut-off filter of 9 has been established, below which the interaction is not exported to UniProtKB and to the Gene Ontology annotation files. Additional rules ensure that any protein pair scoring above 9 must also include at least one evidence of a binary pair, excluding spoke expanded data, before export to UniProtKB/GOA.

These criteria ensure that

  • Only experimental data is used for making the decision to export the protein pair to UniProtKB/GOA as a true binary interacting pair
  • The export decision is always based on at least two pieces of experimental data. A single evidence cannot score highly enough to trigger an export
  • An export cannot be triggered if the protein pair only ever co-occurs in larger complexes, there must be at least one evidence that the proteins are probably in physical contact.

Although these are stringent criteria, it is believed this will make the highest possible quality data available to UniProtKB and GO users. It is our intention to add the binary pairs annotated by other IMEx consortium members as part of the IMEx project to this process in the near future, to increase the data exported out to UniProtKB and GOA. The IntAct group are also happy to make this data available to any other databases who wish to import and display it. Please contact to discuss the most appropriate format for your resource.


How is the intact-miscore calculated?

The IntAct MI score is based on the manual annotation of every instance of a binary interaction (A-B) within the IntAct database. First all instances of the A-B interacting pair are clustered by accession number. Each entry has been annotated using the PSI-CVs and we use this information to score by the interaction detection method and by the interaction type. Additionally we count the number of publications the interaction has appeared in, up to a maximum of 8. Each of these variables is normalised between 0-1. The cumulative score is also normalised between 0-1 across the entire IntAct database, with 1 representing an interaction in which we have the highest confidence.




Data export