Díaz-Montaña Juan J, Gómez-Vela Francisco, Díaz-Díaz Norberto
Intelligent Data Analysis (DATAi), Division of Computer Science, Pablo de Olavide University, ES-41013 Seville, Spain.
Biosystems. 2018 Apr;166:61-65. doi: 10.1016/j.biosystems.2018.01.007. Epub 2018 Feb 14.
Gene networks are currently considered a powerful tool to model biological processes in the Bioinformatics field. A number of approaches to infer gene networks and various software tools to handle them in a visual simplified way have been developed recently. However, there is still a need to assess the inferred networks in order to prove their relevance.
In this paper, we present the new GNC-app for Cytoscape. GNC-app implements the GNC methodology for assessing the biological coherence of gene association networks and integrates it into Cytoscape. Implemented de novo, GNC-app significantly improves the performance of the original algorithm in order to be able to analyse large gene networks more efficiently. It has also been integrated in Cytoscape to increase the tool accessibility for non-technical users and facilitate the visual analysis of the results. This integration allows the user to analyse not only the global biological coherence of the network, but also the biological coherence at the gene-gene relationship level. It also allows the user to leverage Cytoscape capabilities as well as its rich ecosystem of apps to perform further analyses and visualizations of the network using such data.
The GNC-app is freely available at the official Cytoscape app store: http://apps.cytoscape.org/apps/gnc.
基因网络目前被认为是生物信息学领域中用于模拟生物过程的强大工具。最近已经开发出多种推断基因网络的方法以及各种以可视化简化方式处理它们的软件工具。然而，仍然需要评估推断出的网络以证明其相关性。
在本文中，我们展示了用于Cytoscape的新GNC应用程序。GNC应用程序实现了用于评估基因关联网络生物学连贯性的GNC方法，并将其集成到Cytoscape中。GNC应用程序从头开始实现，显著提高了原始算法的性能，以便能够更有效地分析大型基因网络。它还被集成到Cytoscape中，以提高非技术用户对该工具的可访问性，并便于对结果进行可视化分析。这种集成允许用户不仅可以分析网络的全局生物学连贯性，还可以分析基因-基因关系层面的生物学连贯性。它还允许用户利用Cytoscape的功能及其丰富的应用程序生态系统，使用此类数据对网络进行进一步的分析和可视化。
GNC应用程序可在官方Cytoscape应用商店免费获取：http://apps.cytoscape.org/apps/gnc。
