Klein Johannes, Leupold Stefan, Münch Richard, Pommerenke Claudia, Johl Thorsten, Kärst Uwe, Jänsch Lothar, Jahn Dieter, Retter Ida
Institute for Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W460-4. doi: 10.1093/nar/gkn217. Epub 2008 Apr 25.
ProdoNet is a web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. For a given list of genes, the system detects shared operons, identifies co-expressed genes and deduces joint regulators. In addition, the contribution to shared metabolic pathways becomes visible on KEGG maps. Furthermore, the co-occurrence of genes of interest in gene expression profiles can be added to the visualization of the global network. In this way, ProdoNet provides the basis for functional genomics approaches and for the interpretation of transcriptomics and proteomics data. As an example, we present an investigation of an experimental membrane subproteome analysis of Pseudomonas aeruginosa with ProdoNet. The ProdoNet dataset on transcriptional regulation is based on the PRODORIC Prokaryotic Database of Gene Regulation and the Virtual Footprint tool. ProdoNet is accessible at http://www.prodonet.tu-bs.de.
ProdoNet是一个基于网络的应用程序，用于将原核生物基因及相应蛋白质映射到常见的基因调控和代谢网络。对于给定的基因列表，该系统可检测共享操纵子、识别共表达基因并推断联合调控因子。此外，在KEGG图谱上可以看到对共享代谢途径的贡献。此外，感兴趣的基因在基因表达谱中的共现情况可以添加到全局网络的可视化中。通过这种方式，ProdoNet为功能基因组学方法以及转录组学和蛋白质组学数据的解释提供了基础。作为一个例子，我们展示了使用ProdoNet对铜绿假单胞菌实验性膜亚蛋白质组分析的一项研究。ProdoNet关于转录调控的数据集基于PRODORIC原核生物基因调控数据库和虚拟足迹工具。可通过http://www.prodonet.tu-bs.de访问ProdoNet。
