Operons with an upstream FNR ChIP-seq peak and a FNR-dependent change in expression under GMM.

aGenomic location within each FNR ChIP-seq peak with the highest read count (the summit of the peak).bOperon downstream of the FNR ChIP-seq peak, and operon designation was obtained from EcoCyc [70].cIdentification number (B-number) for the first gene in each operon, obtained from EcoCyc [70].dFunctional description of the products of the operons, obtained from EcoCyc [70].eNumber of predicted FNR motifs identified within the FNR ChIP-seq peak region.fLocation of FNR PWM (motif with best PatSer score used if more than one motif identified) relative to the transcription start site (if known). Start site locations obtained from EcoCyc [70] and Kim et al[142].gAnalysis of σ70 occupancy (as determined using ChIP-seq data) under aerobic compared to anaerobic growth conditions. Increases (+) and decreases (−) in σ70 occupancy were statistically determined using a one-sided, paired t-test and p-values were corrected using the Bonferroni method. Also listed are those sites with no σ70 ChIP-seq peaks (Table S2).hThe expression of each operon in WT −O2 cultures was compared to expression in WT +O2 cultures. Each operon was determined to have a significant (>2 fold) increase (+), decrease (−) and no change (o) in WT −O2 relative to WT +O2 (Table S12).iReference for experimentally determined FNR binding at the location of the FNR ChIP-seq peak, if previously identified. Those operons without experimentally determined FNR binding data are marked “None”.jReference for FNR-dependent change in expression of each operon, if previously identified. Those without previous FNR expression data are marked “None”.