Xu Wenjian, Cao Yang, Xie Ziwei, He Haochen, He Song, Hong Hao, Bo Xiaochen, Li Fei
Department of Biotechnology, Beijing Institute of Radiation Medicine, 27 Taiping Street, Haidian District, Beijing, 100850, China.
Tianjin Institute of Health & Environmental Medicine, 1 Dali Road, Heping District, Tianjin, 300050, China.
BMC Bioinformatics. 2017 May 18;18(1):262. doi: 10.1186/s12859-017-1673-1.
Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics data to elaborately construct various context-specific differential molecular networks. However, they cannot easily gain insight into unfamiliar gene networks with the tools that are currently available for pathways resource and network analysis. They would benefit from the development of a standardized tool to compare functions of multiple biological networks quantitatively and promptly.
To address this challenge, we developed NFPscanner, a web server for deciphering gene networks with pathway associations. Adapted from a recently reported knowledge-based framework called network fingerprint, NFPscanner integrates the annotated pathways of 7 databases, 4 algorithms, and 2 graphical visualization modules into a webtool. It implements 3 types of network analysis: Fingerprint: Deciphering gene networks and highlighting inherent pathway modules Alignment: Discovering functional associations by finding optimized node mapping between 2 gene networks Enrichment: Calculating and visualizing gene ontology (GO) and pathway enrichment for genes in networks Users can upload gene networks to NFPscanner through the web interface and then interactively explore the networks' functions.
NFPscanner is open-source software for non-commercial use, freely accessible at http://biotech.bmi.ac.cn/nfs .
已经创建了许多生物途径来表示不同类型的知识，如基因相互作用、代谢反应以及基因调控和物理结合关系。生物学家正在使用广泛的组学数据来精心构建各种特定背景下的差异分子网络。然而，他们无法借助目前用于途径资源和网络分析的工具轻松洞察不熟悉的基因网络。开发一种标准化工具以定量且快速地比较多个生物网络的功能将对他们有所帮助。
为应对这一挑战，我们开发了NFPscanner，一个用于通过途径关联来解读基因网络的网络服务器。NFPscanner改编自最近报道的一个名为网络指纹的基于知识的框架，它将7个数据库的注释途径、4种算法和2个图形可视化模块集成到一个网络工具中。它实现了3种类型的网络分析：指纹识别：解读基因网络并突出内在的途径模块；比对：通过在两个基因网络之间找到优化的节点映射来发现功能关联；富集分析：计算并可视化网络中基因的基因本体（GO）和途径富集情况。用户可以通过网络界面将基因网络上传到NFPscanner，然后交互式地探索网络的功能。
NFPscanner是开源软件，供非商业使用，可从http://biotech.bmi.ac.cn/nfs免费访问。
