Figure 1

Normalized ChIP-chip data. (A+B). Plots of z-scores (see methods) for duplicate ChIP-chip datasets from (A) our study and (B) that of Waldminghaus and Skarstad. Each graph shows z-scores for one replicate dataset plotted against z-scores for the other replicate dataset. Each datapoint shown represents one microarray probe. Datapoints in red represent probes that correspond to σ³² binding sites identified in both studies. Datapoints in blue represent probes that correspond to DSTs. For the Waldminghaus and Skarstad datasets, the nearest probe to the DST coordinate was chosen (the microarray probes for each study are different). Note that some high-scoring probes were not identified as σ³² binding sites because they are adjacent to a probe with an even higher score. (C-H). Plots indicating z-scores for probes within specific genomic regions. (C-E). Regions containing sites of σ³² association identified by our previous work and by Waldminghaus and Skarstad. (F-H). Regions containing DSTs. Data for two replicate experiments from the work of Waldminghaus and Skarstad are shown in orange. Data for two replicate experiments from our previous study are shown in green. Values plotted are the z-scores (see Methods) for each microarray probe in the region. For each plot, associated genes are indicated as blue arrows. Light blue arrows indicate genes for which the site of σ³² association is intragenic, i.e. non-canonical σ³² promoters. Genes with underlined names were not detected in transcriptomic studies of σ³²[17, 18]. The asterisk indicates a ChIP-chip peak that was assigned to the intergenic region upstream of ldhA, the adjacent gene [11]. Note that ldhA was identified as being upregulated by overexpression of σ³²[17].