Fig. 7
Differential expression patterns of canonical and non-canonical TSS. A Number of reliably identified TSS in exponential (exp, orange) and stationary (stat, blue) growth phases visualized for the different culture conditions: LB medium supplemented with 500 mM NaCl (salt), LB medium supplemented with 4 mM L-malic acid (acid), minimal medium (MM), and plain LB medium. Number of TSS are shown for canonical TSS for annotated genes associated with a function (fAG, n = 4866), annotated hypothetical genes (hAG, n = 763), and non-canonical TSS (iTSS, n = 3404; asTSS, n = 5967; oTSS, n = 1130). B Visualization of expression strength (log10 of the mean RRS of three replicates) of transcription start sites of different gene groups in different experimental conditions, as indicated, respectively. C Differentially regulated TSS. Percentage of TSS found not regulated (gray) and regulated (colored) in our experiments. Orange, regulated in LB compared to LB / salt, LB / acid, and minimal medium in exponential phase; blue, regulated in LB compared to LB / salt, LB / acid, and minimal medium in stationary phase; green, regulated between growth phases; yellow, miscellaneous regulation patterns not restricted to either growth conditions or growth phases. D Regulated TSS depending on expression strength (x-axis). Percentage of up-regulated TSS are shown for canonical (gTSS of functional and hypothetical annotated genes: fAG, hAG) and non-canonical TSS (iTSS, asTSS, oTSS). Expression strength classification was adjusted for canonical and non-canonical TSS according the overall expression strength of the TSS as shown in (B). RRS expression strength categories were defined as follows: RRS 1.5-2, 2-2.5, 2.5-3, 3-3.5, 3.5-4, 4-4.5, 4.5-5, 5–10, 10–15, 15–20, 20–30, 30–50, 50–100, > 100. E Comparison of significant regulation of non-canonical asTSS/iTSS in relation to the corresponding canonical gTSS of each annotated gene. Log2(fold change) values of gTSS (x-axis), asTSS (y-axis, left panel) and iTSS (y-axis, right panel) are given. Only data points with significant fold changes of |2|, indicated with black lines, are shown