The tabular view in IntAct

Visualising interactions in IntAct

Now that we have discussed the structure of IntAct and the challenges that come with representing molecular interactions data, let us have a look at how these data are displayed in the IntAct website.

The tabular view allows the visualisation of several interactions together in IntAct.

Figure 11 shows the view that you get once you perform a search for interactions in the IntAct website and it is based in the PSI-MITAB format. This view has the following characteristics:

  • It describes a binary interaction.
  • A binary interaction collapses multiple sets of experimental evidence into a single line.
  •  The order of interactor "A" and "B" is non-deterministic.
  • Whenever the data originates from an n-ary interaction, it is expanded using the Spoke model.

 The view of a search for interactions in the IntAct website

Figure 11. The view of a search for interactions in the IntAct website.

 

[A] Table setting tools: These links allow us to change to different preset table displays or to build a personalised one, in which we can choose which columns are shown using the “Show/hide columns” button, as we will see in the next slide.

[B] Download: Using the drop-down menu we can choose different formats in which to download our data. There is a size constraint and large results will only be available in the tab-delimited format PSI-MITAB.

[C] Column headers: In this basic view a subset of basic fields, including the names of the interacting partners and the method used to find the interaction, is shown. Using the tools described in [A] all the information recorded in an IntAct entry can be displayed as column fields.

[D] Detailed interaction view: following this link (or clicking on the “Interaction AC” as shown in the last column in this view) opens the interaction detail view (see corresponding section).

[E] Links field: If you click on the UniProtKB accession shown for each interacting protein (participant) you will be sent to the relevant UniProt entry. If the participant is not a protein, but a small molecule, for example, you will find a ChEBI identifier in this place. Each participant is also assigned a unique EBI identifier that is shown in the links field. If you click on this identifier, you will be re-directed to a Dasty2 visualisation page. We will learn more about Dasty visualisation later.

The next slide will show other display columns including a method of expansion, allowing you to filter out columns:

 

Changing the view

Here we have a more detailed view of the display options (Figure 12).

As you can see in the magnified section [A], with the “Show/hide columns” menu you can choose precisely which columns to show, accessing information such as interacting partners alias, interaction detection methods or interaction confidence scores. Either from this menu or from the “Change table preset…” one [B], you can also use pre-determined displays that range from the minimal view, showing only the names of the interactors and the accession to the interaction, to the expanded view, which shows 26 different fields comprising most of the information referred to the interaction.  

A detailed view of the display options

Figure 12. The display options. [A] “Show/hide columns” menu. [B] “Change table preset...” menu.