Conclusion
We believe our results on E. coli demonstrate the viability of the multi-method approach for bacteria. The focus on gene/TF interactions rather than the gene/gene interaction approach apparently is a key to the approach and also yields more detailed information on the nature of the TRN. The Bayesian framework provides the objective interaction methodology.
The multi-method integration scheme straightforwardly generalizes to other techniques; thus we are presently adding promoter analysis and protein-protein interaction modules to the integrated scoring. We hope this type of computational analysis will guide experimental studies and accelerate research in the discovery of TRNs. We are applying the methodology to other bacteria of interest, notably Geobacter sulfurreducens and Bacillus anthracis.