Comparison of GRN topology from previous studies with the RosR regulon characterized here. (A) Subnetwork diagram depicting predictions regarding putative VNG0258H function from the ROS environmental gene regulatory inference network (EGRIN) (adapted from ). Circles represent transcription factor (TF) groups. TF group 23 includes VNG0258H and four other putative TFs (VNG0101G, VNG0347G, VNG1496G, and VNG0890G). Diamonds represent combinatorial logic gates (AND). Blunt arrows represent computationally inferred repression influences, whereas pointed arrows are activation influences. Squares represent inferred clusters of co-regulated genes and numbers within the squares refer to EGRIN cluster IDs. (B) Refinements to GRN model based on the work presented in the current study. Node shapes and edge attributes are as in (A). Solid lines indicate direct regulation (i.e. DNA-protein interaction has been detected), whereas dotted lines represent interactions that could be direct or indirect (i.e. direct interaction still needs to be tested). Dark grey boxes within light grey boxes indicate that, out of all genes in the cluster, only the gene indicated in dark grey is RosR-dependent based on the microarray data from the current study.
Sharma et al. BMC Genomics 2012 13:351 doi:10.1186/1471-2164-13-351