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:
from: DOI: 10.1016/j.cell.2020.05.032
For the network diagram of the enrichment results:
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
Apps menu -> App Manager -> find ClueGO -> Install
Request a license key
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.
GO enrichment as an example:
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
For other databases, such as KEGG, the steps are similar.