Figure 11.

PhoPQ gene regulatory pathway Manually-curated comprehensive gene regulatory pathway network for the phoPQ system. The two component pathway involves transcriptional regulation of 44 genes, 5 of which are involved in another cascading two component system (pmrBA). A positive feedback loop exists in this pathway, in the form of up regulation of phoPQ gene by the system. The figure shows the complete pathway, with the positive feedback loop marked in dark color. The pathways have been constructed using the Cell Designer 3.0 software which presents a structured (Extensible Markup Language (XML)) format data that can be easily rendered into the discrete event simulation framework. The process involved 112 experimental reports of this system extracted from PubMed [57], development of the pathway graphs for each experiment and then concatenating those graphs to get the complete pathway graph.

Ghosh et al. BMC Genomics 2010 11(Suppl 3):S3   doi:10.1186/1471-2164-11-S3-S3