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
Apps
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ClueGo
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Getlicense
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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.
Take 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
Start analysis:
For other databases, such as KEGG, the steps are similar.