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Moreover, this section provides information on gene regulation and the corresponding regulators and their regulatory mechanisms.
GenDB now visualizes all known regulatory interactions (retrieved from CoryneRegNet) for a chosen region combined with several links to the corresponding regulators, target genes, and known co-regulated genes (exemplarily shown in Figure 2 for ramB, a transcriptional regulator of the MerR family).
The observations indicate that these transcriptional repressors should commonly adopt the unique recognition mode as observed in RolR to interact with corresponding regulators, which may take certain resorcinol-like compounds as their effector molecules.
To summarize, the general concept is to use topological properties of the global protein interaction network to identify non-local regulation patterns and associate a set of putative targets with each signaling molecule of interest, then assess expression profiles of these targets and infer activity of corresponding regulators.
Crosstalk motifs were defined as the private target gene sets of two corresponding regulators, TFs and/or miRNAs, which shared at least two targets.
The continuous gene expression profiles in Figure 11 [also see Additional file 5] are generated by the identified dynamic model for all target genes and their corresponding regulators, which can fit the microarray data reasonably well.
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Locus tag, Name of TF, Size and FDR q-val represent the gene ID, the corresponding regulator gene, the number of regulated downstream genes and the statistical significance, respectively.
A set of targets enriched in differentially expressed genes would imply activity of corresponding regulator(s).
A potential radiation-desiccation response regulon and the corresponding regulator common to D. radiodurans and D. geothermalis were identified using the approach developed by Mironov et al [99], [100].
These systems typically consist of a sensor protein with a membrane-bound histidine kinase domain (HisKA) and a corresponding regulator protein with a response regulator domain (RR).
Putative Response Regulator: Additional predictive evidence for this diverged TCS became available by searching for a corresponding regulator protein: This search was initiated by an organism specific iterative BLAST with NarL from P. arcticus.
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