Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W505-9. doi: 10.1093/nar/gks445. Epub 2012 May 25.
High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular descriptions of cellular responses to perturbations. However, it is difficult to integrate these diverse data to reconstruct biologically meaningful signaling networks. Previously, we have established a framework for integrating transcriptional, proteomic and interactome data by searching for the solution to the prize-collecting Steiner tree problem. Here, we present a web server, SteinerNet, to make this method available in a user-friendly format for a broad range of users with data from any species. At a minimum, a user only needs to provide a set of experimentally detected proteins and/or genes and the server will search for connections among these data from the provided interactomes for yeast, human, mouse, Drosophila melanogaster and Caenorhabditis elegans. More advanced users can upload their own interactome data as well. The server provides interactive visualization of the resulting optimal network and downloadable files detailing the analysis and results. We believe that SteinerNet will be useful for researchers who would like to integrate their high-throughput data for a specific condition or cellular response and to find biologically meaningful pathways. SteinerNet is accessible at http://fraenkel.mit.edu/steinernet.
高通量技术，包括转录谱分析、蛋白质组学和反向遗传学筛选，为细胞对干扰的反应提供了详细的分子描述。然而，将这些多样化的数据整合起来以重建具有生物学意义的信号网络是很困难的。之前，我们已经建立了一个整合转录组学、蛋白质组学和相互作用组数据的框架，通过搜索奖收集 Steiner 树问题的解决方案来实现这一点。在这里，我们提出了一个网络服务器，SteinerNet，以一种用户友好的格式为广泛的用户提供这个方法，这些用户的数据来自任何物种。用户只需提供一组实验检测到的蛋白质和/或基因，服务器就会从酵母、人类、小鼠、黑腹果蝇和秀丽隐杆线虫提供的相互作用组中搜索这些数据之间的连接。更高级的用户也可以上传自己的相互作用组数据。该服务器提供了生成的最优网络的交互式可视化以及详细的分析和结果的可下载文件。我们相信，SteinerNet 将对那些希望整合特定条件或细胞反应的高通量数据并找到具有生物学意义的途径的研究人员有用。SteinerNet 可在 http://fraenkel.mit.edu/steinernet 访问。
