Comparison of gene expression maps from available S Comparison of gene expression maps from available S. mutans competence transcriptome studies. Comparison of gene expression maps from available S. mutans competence transcriptome studies. The directions of the activated TARs (arrows) from S. mutans exposed for 100 min to CSP are indicated by arrows as follows: red, TARs of the ComE regulon; green, the ComR regulon; blue and black, TARs of the SigX regulon with 5′ ends starting in the sense and antisense directions, respectively. The genes proximal to the ComE DR are red, those proximal to the ComR indirect repeat are green, and those proximal to the SigX box are blue. Gene numbers are as in the sequence with GenBank accession no. AE014133. Gene expression data for corresponding regions are indicated for five transcriptome studies, as indicated at the left. The top row is UA159 (100 min). The transcriptomes in studies 1, 3, and 5 used traditional microarrays with probes limited to annotated ORFs (15, 32, 39). The transcriptome in study 2 used a tiling microarray covering most of the S. mutans genome (28). Study 4 used RNA sequencing in the analysis of the response to CSP and XIP in CDM (27). The CSP response in this medium does not support activation of competence but is included for comparative analysis of early responses. The transcriptome for XIP in CDM used a 30-min exposure to XIP, which was probably too short to detect the full range of core genes regulated by SigX. The comS gene was not represented in the arrays for the transcriptomes in studies 1, 2, 3, and 5 (empty space). R. Khan et al. mSystems 2016; doi:10.1128/mSystems.00038-15