Visualising the output

If your results table is too big, the web tool will not be able to represent them and you will need to download your data as explained before in a Cytoscape-compatible format (XGMML would be the best choice) in order to represent it there.

[A]  If your results table is not too long (roughly below 500 interactions), you can have a quick look at your data by producing a simple graphical representation using the “Graph” tab  (Figure 23).
This opens the Network visualisation window and shows a network representation of your interactions using CytoscapeWeb (infobox below). Each interacting molecule is represented as a node (the little balls in the graph) that is linked to other node(s) by an edge, the connecting line that represents the interaction.

Network visualisation window

Figure 23. Network visualisation window. [A] The Graph tab. [B] Open in Cytoscape. [C] CytoscapeWeb Controls.

[B]  Open in Cytoscape: If you want to produce a more complex visualisation, making use of Cytoscape advanced representation options, you can export your representation to Cytoscape Webstart.  You can also download your dataset in XGMML format (an XML-based format specifically designed for Cytoscape) as shown in 'How do I get data from IntAct' and then import it into your favourite version of Cytoscape.

[C]  CytoscapeWeb controls: CytoscapeWeb has limited visualisation options but you can can use the Cytoscape Web controls box to choose between three different layouts and to represent each piece of evidence for an interaction as a single edge by deactivating the “merge edges” feature. Each edge represents one interaction detected in one publication using one specific methodology, but they are merged by default when more than one instance of an interaction is found. By deactivating this feature, you can easily see which interactions have been found more than once.


  • CytoscapeWeb is a web-based network visualisation tool.
  • It is modelled on Cytoscape: it is open-source, interactive, customisable and easily integrated into web sites.
  • CytoscapeWeb contains none of the plugin functionality of Cytoscape, nor its advanced representation options.