Visualization of protein interaction networks: problems and solutions.
Visualization of protein interaction networks: problems and solutions.
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DOI：
10.1186/1471-2105-14-s1-s1
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发表时间：
2013
影响因子：
3
通讯作者：
Cannataro M
中科院分区：
文献类型：
--
作者：
Agapito G;Guzzi PH;Cannataro M
可视化涉及数据的可视化表示，是科学研究中的一项重要任务。蛋白质-蛋白质相互作用（PPI）的发现要么使用湿实验室技术，如质谱，要么使用计算机预测工具，导致大量相互作用的集合存储在专门的数据库中。生物体所有相互作用的集合形成蛋白质-蛋白质相互作用网络（PIN），是研究细胞机制行为的重要工具。由于pin的图形表示可能会突出重要的子结构，例如蛋白质复合物，因此越来越多地使用可视化来研究pin的底层图结构。虽然图是众所周知的数据结构，但关于pin可视化存在不同的开放问题：大量的节点和连接，节点（蛋白质）和边缘（相互作用）的异质性，注释蛋白质的可能性以及与本体（例如基因本体）提取的生物信息的相互作用，这些信息丰富了pin的语义信息，但使其可视化变得复杂。在过去的几年里，已经开发了许多用于pin可视化的软件工具。最初的想法只是为了可视化，其中一些已经陆续丰富了新的功能，用于PPI数据管理和PIN分析。本文分析了pin码可视化的主要软件工具，考虑了四个主要标准：(i)技术，即软件的可用性/许可和支持的OS（操作系统）平台；（ii）互操作性，即以不同格式导入/导出网络的能力、以图形格式导出数据的能力、系统的可扩展性（例如通过插件）；（iii）可视化，即支持的布局和渲染算法以及并行实现的可用性；（iv）分析，即网络分析功能的可用性，如聚类或图挖掘，以及与外部数据库交互的可能性。目前，市面上有很多工具可供选择，用户很难从中选择一个。一些工具提供复杂的2D和3D网络可视化，使许多布局算法可用，其他工具更面向数据，支持来自不同来源的交互数据和数据注释的集成。最后，一些专门的工具专门用于分析途径和细胞过程，并面向系统生物学研究，其中正在研究的过程的动态方面是中心。当前的一个趋势是部署开放的、可扩展的可视化工具（例如Cytoscape），通过开发插件，interactomics社区可能会逐渐丰富这些工具，为PIN分析提供新颖而更强大的功能。另一方面，另一个新兴趋势是可视化引擎的高效并行实现，它可以提供高交互性和接近实时的响应时间，如NAViGaTOR。从技术的角度来看，开源、免费和可扩展的工具，如Cytoscape，由于开发人员和用户社区的庞大，保证了长期的可持续性，并提供了很大的灵活性，因为开发人员社区通过新的插件不断添加新功能，但新兴的并行、通常是封闭源的工具，如NAViGaTOR，也可以在分析非常大的pin时提供接近实时的响应时间。
Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization. In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to interact with external databases. Currently, many tools are available and it is not easy for the users choosing one of them. Some tools offer sophisticated 2D and 3D network visualization making available many layout algorithms, others tools are more data-oriented and support integration of interaction data coming from different sources and data annotation. Finally, some specialistic tools are dedicated to the analysis of pathways and cellular processes and are oriented toward systems biology studies, where the dynamic aspects of the processes being studied are central. A current trend is the deployment of open, extensible visualization tools (e.g. Cytoscape), that may be incrementally enriched by the interactomics community with novel and more powerful functions for PIN analysis, through the development of plug-ins. On the other hand, another emerging trend regards the efficient and parallel implementation of the visualization engine that may provide high interactivity and near real-time response time, as in NAViGaTOR. From a technological point of view, open-source, free and extensible tools, like Cytoscape, guarantee a long term sustainability due to the largeness of the developers and users communities, and provide a great flexibility since new functions are continuously added by the developer community through new plug-ins, but the emerging parallel, often closed-source tools like NAViGaTOR, can offer near real-time response time also in the analysis of very huge PINs.