The interaction detail view in IntAct

Accessing the interaction detail view

To open the Interaction detail view click on the magnifying glass link [A]  or on the appropriate “Interaction AC”  [B] displayed in the last column of the table described in Tabular View, see Figure 13. Either of these actions will direct you to the interaction view.

 The view of a search for interactions in the IntAct website

Figure 13. The view of a search for interactions in the IntAct website.

Let's have a look at the interaction detail view.

Detailed view of the interaction tables - Overview

The interaction detail view follows the general IntAct schema described in 'How is data stored in IntAct?'.  Each level of the schema has a different section in the interaction view. Let's look through these levels in more detail (Figure 14).

 

The first two levels of data in the interaction detail view

Figure 14. The first two levels of data in the interaction detail view: [A] Experiment, [B] Publication.

[A] Experiment level: you can see how many interactions are found in the experiment where the interaction of interest was found. Here you can learn which organism the experiment was performed in and the method used to find the interaction, as well as the method used to identify the interaction participants.

[B] Publication level: this level provides a reference to the article in which the experiment was published. The publication is the highest level of an IntAct database entry, so you can also find other information on the database entry here. These may include comments on the origin of the data if was not present in the publication but was registered by the submitter or added through deep curation. There is also a link to all the interactions found in the same publication.

We will continue the description of further levels on the next page.

Detailed view of the interaction tables - Overview

Continuing view of the interaction table (Figure 15):

Further levels of Interaction Details

Figure 15. Further levels of Interaction Details :[C] Interaction, [D] Participants, [E] Graphical representation of experimental features.

[C] Interaction level: here the name and accession code of the interaction are listed. There is also information about what type of interaction we are dealing with, whether it is a direct interaction, an enzymatic reaction, some type of physical association, etc… The figure or table in the article in which the interaction data is given is also shown here.

[D] Participant level: this provides a detailed representation of the participants in the interaction. We will describe this in more detail in the next slide.

[E] Graphical representation of experimental features: this provides a simplified graphical view of the interaction, which we will describe in more detail in the next slide. In this particular example the second interactor has a mutation.

Detailed view of the interaction tables - Interaction Representation

Here we describe how the interaction is represented:

The contents of the interaction, participant and feature levels give us detailed information about the interacting molecules and their relationship (Figure 16).

Detailed information about the interacting molecules and their relationship

Figure 16. Detailed information about the interacting molecules and their relationship. Participant's descriptions: [A] Identifiers, [B] Organism of origin, [C] Type of molecule, [D] Biological role, [E] Role in interaction, [F] More links: Features (highlighted) [Graphical representation of the "More" features will be explained below].

[A]  Image shows the actual participants of the interaction and their identifiers.

We can also see information about:

  • their organism of origin [B],
  • their experimental role in the interaction (e.g. bait or prey) [C],
  • their biological role (e.g. enzyme or enzyme substrate) [D],
  • their type (e.g. protein or small molecule) [E],

The final column [F], labelled "more", allows access to extra information on: annotations (indicated with an A), experimental parameters (indicated with an P), such as binding affinities,  stochiometric values (indicated with an S) and features (indicated with an F).  The latter can be particularly interesting as shown in Figure 17 below see: [G].

Graphical representation of experimental features

Figure 17. The features can comprise labelling tags, binding regions or any modification that the interacting molecule might have. The graphical display allows simple representation of binding regions and other experimental features that the molecules might have, as explained in the help box magnified here.

 

Next, we will explain how to search IntAct.