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Bioinformatics. 2019 Oct 1;35(19):3864-3866. doi: 10.1093/bioinformatics/btz163.

Automated exploration of gene ontology term and pathway networks with ClueGO-REST.

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INSERM, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre le Cancer, Sorbonne Université, Université Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, Paris F-75006, France.
Inovarion, Paris 75013, France.



Large scale technologies produce massive amounts of experimental data that need to be investigated. To improve their biological interpretation we have developed ClueGO, a Cytoscape App that selects representative Gene Onology terms and pathways for one or multiple lists of genes/proteins and visualizes them into functionally organized networks. Because of its reliability, userfriendliness and support of many species ClueGO gained a large community of users. To further allow scientists programmatic access to ClueGO with R, Python, JavaScript etc., we implemented the cyREST API into ClueGO. In this article we describe this novel, complementary way of accessing ClueGO via REST, and provide R and Phyton examples to demonstrate how ClueGO workflows can be integrated into bioinformatic analysis pipelines.


ClueGO is available in the Cytoscape App Store (


Supplementary data are available at Bioinformatics online.

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