Figure 1. Overview of Our Approach for Mapping the E. coli Transcriptional Regulatory Network.

Microarray expression profiles were obtained from several investigators. Our laboratory profiled additional conditions, focusing on DNA damage, stress responses, and persistence. These two data sources were combined into one uniformly normalized E. coli microarray compendium that was analyzed with the CLR network inference algorithm. The predicted regulatory network was validated using RegulonDB, sequence analysis, and ChIP. The validated network was then examined for cases of combinatorial regulation, one of which was explored with follow-up real-time quantitative PCR experiments.