Fig. 2

Reliability of TSS identification. A Distribution of the distances of the TSS (minRRS ≥ 5) to the start codon within a 500-bp window upstream of 4342 annotated genes associated to a function (fAG, upper panel) and 657 hypothetical genes (hAG, lower panel). The distance between TSS and start codons is given in nucleotides (nt). Box-plots above each panel display minimum (0 bp), maximum (500 bp), 25th percentile (33 and 40 bp), median (83 and 139 bp), and 75th percentile (247 and 317 bp) of the 5′ UTR lengths, respectively. B Comparison of TSS between EHEC and E. coli K12 MG1655. TSS of 1682 homologous genes of EHEC and E. coli K12 MG1655 were analyzed. The frequency of genes with a deviation (specified below each bin) of the distance between start codon and TSS is shown as absolute numbers (left y-axis) and as cumulative function (right y-axis). C Classification scheme for TSS used in this study. TSS groups comprise ‘gTSS’, gene associated TSS upstream of the start codon of annotated genes; ‘iTSS’, sense internal TSS within annotated genes; ‘asTSS’, TSS antisense of the coding region of annotated genes or their 5’ UTR (u-asTSS) or 3’ UTR (d-asTSS); and ‘oTSS’, orphan TSS without association to annotated genes