How to plot Enrichment Network Diagram with Cytoscape/ClueGO

created at 06-29-2021 views: 88

This omics article about coronavirus published on cell in 2020 contains a lot of Bioinformatics. Today I will take you to reproduce one of the Supplemental Figures: 

Protein Interaction Network

Protein Interaction Network

from: DOI: 10.1016/j.cell.2020.05.032

Understand the diagram

For the network diagram of the enrichment results:

  • nodes represent representative enrichment pathways,
  • lines between nodes indicate the number of genes shared between the pathways,
  • color indicates the enrichment classification of the node (which functional group it belongs to, the color can also correspond to the ClueGO result in the form of a table).


Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways, and integrating these networks with annotations, gene expression profiles, and other status data. The Cytoscape core distribution provides a set of basic features for data integration, analysis, and visualization. Other functions can also be used as plug-ins. Plug-ins can be used for network and molecular analysis, new layouts, additional file format support, scripts and connections to databases.


ClueGO is a Cytoscape plugin that can visualize non-redundant biological terms of large clusters of genes in a functionally grouped network. The identifier can be uploaded from a text file or interactively from the Cytoscape network. Users can easily extend the supported identifier types. ClueGO performs single cluster analysis and comparison of several clusters (gene lists). From the ontology source used, the terms are selected according to different filtering criteria.


1. Download Cytoscape

2. Download the ClueGO plugin

Apps menu -> App Manager -> find ClueGO -> Install

Download the ClueGO plugin

3. ClueGO activation

Apps - ClueGo - Getlicense - Request a license key

ClueGO activation

Submit the review after filling in the basic information, the review time may take 1 day. After receiving the license in the email, click App-ClueGO- Re-license, and enter the license in the pop-up prompt box to activate ClueGO.


4. Upload data

Upload data

  • 1:Species
  • 2:Paste gene id, symbol, protein id, etc.
  • 3:import file

5. Select the enrichment data set and enrichment criteria

Take GO enrichment as an example:

 GO enrichment

During the enrichment process, the p value will be calculated by the hypergeometric method. Here you can choose the value of p less than 0.05, and display this part of the result

hoose the value with p

Start analysis:

Start analysis

6. Results


For other databases, such as KEGG, the steps are similar.

created at:06-29-2021
edited at: 07-08-2021: