Enrichment Table App
The Enrichment Table App provides the
functionality of functional enrichment analysis
for any network loaded into Cytoscape using g:Profiler's web service.
This tutorial includes a basic workflow for visualizing enrichment data on pathways and networks in
- Install and launch the latest version of Cytoscape.
- Install the Enrichment Table app via Apps → App Store ....
- Search for mouse TF pathway in NDEx and and pick top option with title
Ravasi et al., CELL (2010) - Mouse TF interactions which would be used as an
examples to demonstrate different features of the app.
Initialise Enrichment Table App
- Open the Ravasi et al., CELL (2010) - Mouse TF interactions network.
- Select the Enrichment Table option from table panel
- You would be greeted with a screen similar to below
Organism And Gene ID Prediction
Enrichment process requires two mandatory parameters:
Organism: Organism associated with the query genes
Gene ID: Node table column containing the gene symbols
Both these parameters are predicted by enrichment table app if enough information is available
Running Enrichment Process
Click the Perform Gene Enrichment button with icon of reload. This you provide
you with the table containing enrichment results. The results are sorted according to the p-value in a increasing order.
Filtering Table Data
There are couple of parameters based on which you can filter the table
- Click the Filter Enrichment Table button with filter icon to access the
- Select Gene Ontology Biological Process in the categories. Click ok. You
will see a filtered table, along with number of current rows a label above table.
- Open to filter panel again and check remove redundant terms. Click ok to see terms consisting of
both filters applied.
Ring charts provide ability visualise top-5 terms in the network using split-charts. You can change
the number of terms and type of chart in chart setting panel.
- Click Draw Chart to create chart with default setting and split charts
will appear in the network.
- To remove the chart, click on Reset Charts to remove charts
- To change charts setting, go to Visit the network specific chart settings
- To visualize one or more enrichment term, select the rows in the table and the corresponding
nodes will get highlighted.
- Similarly, select a group of nodes in the network and only the rows that contains atleast all of
the selected nodes will be present in the table.
Advanced Enrichment Settings
In addition to Organism and Gene ID column, there are
other parameters that can be changed to obtain a more precise enrichment results.
The Options are available in the Network specific enrichment panel settings
section which can be accessed by clicking the
Enrichment Map Generation
We can generate Enrichment Map from the enrichment data
generated by our app. This requires Enrichment Map to be
installed in Cytoscape.
Once, enrichment map app is present, click enrichment map icon and which will provide a panel to change the file
name and connectivity cutoff, and click ok to generate map.
Exporting Enrichment Table
Enrichment Table App provides functionality to export the data:
- Select the icon that will open the export panel.
- Select appropriate location and file name and save the table.