Salamon John, Goenawan Ivan H, Lynn David J
EMBL Australia Group, Infection and Immunity Theme, South Australian Medical and Health Research Institute, North Terrace, Adelaide, South Australia, Australia.
College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.
Curr Protoc Bioinformatics. 2018 Sep;63(1):e55. doi: 10.1002/cpbi.55. Epub 2018 Aug 31.
Biological processes are regulated at a cellular level by tightly controlled molecular interaction networks, which are collectively known as the interactome. The interactome is not a static entity, but instead is dynamically reorganized or "rewired" under varying temporal, spatial, and environmental conditions. Most network analysis and visualization tools have, to date, been developed for static representations of molecular interaction data. Here, we describe a protocol that provides a step-by-step guide to DyNet, a Cytoscape 3 application that facilitates the visualization and analysis of dynamic molecular interaction networks. DyNet represents a dynamic network as a set of state graphs that are synchronized in their layout. This synchronization is managed in real time and is automatically updated when a graph is manipulated by a user (e.g., dragging, zooming, moving a node). DyNet also provides several statistical tools enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. © 2018 by John Wiley & Sons, Inc.
生物过程在细胞水平上由严格控制的分子相互作用网络调节，这些网络统称为相互作用组。相互作用组不是一个静态实体，而是在不同的时间、空间和环境条件下动态重组或“重新布线”。迄今为止，大多数网络分析和可视化工具都是为分子相互作用数据的静态表示而开发的。在这里，我们描述了一个协议，该协议为DyNet提供了逐步指导，DyNet是一个Cytoscape 3应用程序，有助于动态分子相互作用网络的可视化和分析。DyNet将动态网络表示为一组在布局上同步的状态图。这种同步是实时管理的，并且当用户操作图形（例如拖动、缩放、移动节点）时会自动更新。DyNet还提供了几种统计工具，使用户能够快速识别和分析许多网络状态中最“重新布线”的节点。© 2018 John Wiley & Sons, Inc.
