Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks.
复制标题
DOI：
10.1186/s12859-015-0863-y
复制
发表时间：
2016-01-05
影响因子：
3
通讯作者：
Van de Peer Y
中科院分区：
文献类型：
--
作者：
Van Landeghem S;Van Parys T;Dubois M;Inzé D;Van de Peer Y
差分网络最近被引入作为一个强大的方式来研究动态的重新布线能力的相互作用组在不断变化的环境条件或刺激。目前，这种差分网络是使用自组织方法生成和可视化的，并且通常仅限于一次分析一种特定条件的响应或一种交互类型。在这项工作中，我们提出了一个通用的，本体驱动的框架来推断，可视化和分析一组任意的条件特定的反应对一个参考网络。为此，我们已经实现了新的基于本体的算法，可以处理高度异构的网络，占物理相互作用和监管协会，对称和定向边缘，边缘权重和否定。我们提出这个综合框架作为一个标准化的方法，允许差分网络的统一观点，并促进差分网络研究之间的可比性。作为一个说明性的应用，我们证明了它的有用性，植物非生物胁迫研究，我们实验证实了预测的调节器。Diffany作为开源Java库和Cytoscape插件可以从http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/免费获得。本文的在线版本（doi：10.1186/s12859-015-0863-y）包含补充材料，可供授权用户使用。
Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such differential networks are generated and visualised using ad hoc methods, and are often limited to the analysis of only one condition-specific response or one interaction type at a time. In this work, we present a generic, ontology-driven framework to infer, visualise and analyse an arbitrary set of condition-specific responses against one reference network. To this end, we have implemented novel ontology-based algorithms that can process highly heterogeneous networks, accounting for both physical interactions and regulatory associations, symmetric and directed edges, edge weights and negation. We propose this integrative framework as a standardised methodology that allows a unified view on differential networks and promotes comparability between differential network studies. As an illustrative application, we demonstrate its usefulness on a plant abiotic stress study and we experimentally confirmed a predicted regulator. Diffany is freely available as open-source java library and Cytoscape plugin from http://bioinformatics.psb.ugent.be/supplementary_data/solan/diffany/. The online version of this article (doi:10.1186/s12859-015-0863-y) contains supplementary material, which is available to authorized users.