使用 ClueGO-REST 自动探索基因本体论术语和途径网络。
Automated exploration of gene ontology term and pathway networks with ClueGO-REST.
机构信息
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.
出版信息
Bioinformatics. 2019 Oct 1;35(19):3864-3866. doi: 10.1093/bioinformatics/btz163.
SUMMARY
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.
AVAILABILITY AND IMPLEMENTATION
ClueGO is available in the Cytoscape App Store (http://apps.cytoscape.org/apps/cluego).
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
大规模技术产生了大量需要研究的实验数据。为了提高其生物学解释能力，我们开发了 ClueGO，这是一个 Cytoscape App，可选择一个或多个基因/蛋白质列表的代表性基因本体术语和途径，并将其可视化到功能组织的网络中。由于其可靠性、用户友好性和对许多物种的支持，ClueGO 获得了大量的用户群。为了进一步允许科学家使用 R、Python、JavaScript 等以编程方式访问 ClueGO，我们将 cyREST API 集成到 ClueGO 中。在本文中，我们描述了通过 REST 访问 ClueGO 的这种新颖的、互补的方式，并提供了 R 和 Phyton 的示例，以演示如何将 ClueGO 工作流程集成到生物信息学分析管道中。
可用性和实现
ClueGO 可在 Cytoscape App Store（http://apps.cytoscape.org/apps/cluego）中获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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