List Markus, Alcaraz Nicolas, Dissing-Hansen Martin, Ditzel Henrik J, Mollenhauer Jan, Baumbach Jan
Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.
Nucleic Acids Res. 2016 Jul 8;44(W1):W98-W104. doi: 10.1093/nar/gkw373. Epub 2016 May 5.
We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment analysis directly in the browser. Given a biological interaction network (e.g. protein-protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression, for instance), KeyPathwayMiner extracts connected sub-networks containing a high number of active or differentially regulated genes (proteins, metabolites) in the molecular profiles. The web interface at (http://keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set such as data integration, input of background knowledge, batch runs for parameter optimization and visualization of extracted pathways. In addition to an intuitive web interface, we also implemented a RESTful API that now enables other online developers to integrate network enrichment as a web service into their own platforms.
我们展示了KeyPathwayMinerWeb,这是首个可直接在浏览器中进行从头通路富集分析的在线平台。给定一个生物相互作用网络(例如蛋白质-蛋白质相互作用)以及一系列源自一项或多项组学研究的分子谱(例如基因表达),KeyPathwayMiner会提取在分子谱中包含大量活跃或差异调节基因(蛋白质、代谢物)的连通子网络。网址为(http://keypathwayminer.compbio.sdu.dk)的网络界面实现了KeyPathwayMiner工具集的所有核心功能,如数据整合、背景知识输入、用于参数优化的批量运行以及提取通路的可视化。除了直观的网络界面,我们还实现了一个RESTful API,现在它使其他在线开发者能够将网络富集作为一项网络服务集成到他们自己的平台中。