Example 3: Find the biological role of your network

Some biological analysis tools give a network as a result. The next step in these cases is to identify the biological functions behind it. In the following line we describe how to do a Gene Ontology Enrichment Analysis to gain insight into the function of your network. The network we will study can be downloaded here

Step 1: Go to Single Enrichment Analysis

Load your network and open Analysis > Functional > Single Enrichment

Step 2: Choose what you are going to compare

First, select compare a list versus the whole genome analysis. If instead of using the whole genome as a reference space you have another reference, choose list 1 versus list 2 and upload the list of genes or proteins from your referente space.

Secondly, select the genes you want to study for enrichment. In this case are all the nodes from your network but it can be a subset.

Step 3: Select the specie and the GO domain you want to study

Step 4: Select the output folder

Select the output folder in the workspace where the results are going to be saved.

Step 5: Run the analysis

Step 6: Check the status of your analysis

Go to the Jobs button in the upper right side of the blue header and a new panel will appear with all the jobs that you have launched.

When the analysis finished, the job will be labelled as "Ready"

Step 7: Explore the results

At the results form, the first section gives you a description of your analysis:

Secondly, there is a table summarising the significant GO functional terms found to be enriched in your network:

The GO results are displayed as GO graphs where the significant functional terms are highlighted in a way that the stronger the color is, the more significant is the GO term in the comparison (red fro over-represented terms and blue for the under-represented). There is a different GO network for each GO domain you are analysing (GO cellular component, GO molecular function, GO biological process).

Step 8: Explore the GO significant network

Explore the GO network. If you put the mouse cursor over a node and click the right button, a pop-up box will appear with the pvalue of the GO term.

Step 9: Save the GO network as a session and open it the main CellMaps

Finally, you can save each network as a CellMaps session.

This sessions can be open in the main CellMaps page for a more efficient exploration. Go to the main menu File > Manage sessions, look for the GO network you saved and open it.