The human signalosome complex

Initial simple search

Imagine that you are interested in the human signalosome complex, a multifunctional protein complex essential for development and possibly involved in the regulation of protein degradation. You want to generate a network that will show the proteins that are known to physically interact to form the complex or regulate its function.

Since IntAct supports searching with terms coming from Gene Ontology, we can use “signalosome” (a GO term) to perform a simple search using the search bar [A]. 993 binary interactions are found, as you can see in the close-up (Figure 24).

However you want to refine the search because you want to study the signalosome in humans, not in other organisms.

Performing a simple search on IntAct

Figure 24. Performing a simple search on IntAct.

Search refinement (1)

To refine the search and limit it to those interactions that involve human proteins*, we make use of the advanced fields of the IntAct search box (Figure 25).

*Sometimes you will find interactions in IntAct involve proteins from two different organisms. This may be the case if, for example, a researcher does not have a purified human protein but wants to find out which other human proteins it interacts with.  In such studies, homologues from other species such as mouse may be used as a substitute for the human protein. 

Refining your search

Figure 25.  Refining your search.  

Steps

 

  1. Click the “Show Advanced Fields” link [A]. An extension of the search box appears below it.
  2. From the extension box use a drop-down menu [B] to select “organism”. 
  3. Type  "human" (or "Homo sapiens") into the "Add & Search" box to limit your results to interactions involving human proteins.

 

Search refinement (2)

In the close-up we can see how the number of interactions has gone down to 339. Our results are now limited to those interactions that involve human proteins. However, if we have another look at the close-up we see that a significant number of these interactions come from spoke expanded co-complexes (see Figure 10). As some of these may be false positives, we can filter them out to get a list of binary interactions. For that, we click on the “filter” link as underlined in red (Figure 26).

Filtering your refined search results

Figure 26.  Adding a filter to your refined search results.

Filtering spoke expanded expansions

Notice that the whole process can be summarized by a direct MIQL query as depicted in the search bar (Figure 27) [A].

After we have finished filtering our results, we end up with 168 interactions [B] involving human proteins annotated to be related to the signalosome.

Your filtered results

Figure 27.  Your filtered results.

We can now download the results using the download drop-down menu and button [C].

Alternatively we can represent the network using the “Graph” tab [D] (shown in the next slide).

 

Graphical representation of the signalosome network

Finally, here we have the representation of the signalosome-related interactions as given by IntAct (Figure 28). This can be used as a starting point to help you unveil the relationships between the different proteins involved in the complex. The CytoscapeWeb Controls box [A] can be used to try different layouts and see if you can represent the networks in a more informative fashion.

A graphical representation of the signalosome-related interactions

Figure 28.  A graphical representation of the signalosome-related interactions.