Extended Data Fig. 2: Relationships between Transcription Induced Domains and CIDs.
a, E coli contact map binned at 5 kb at the top. Below the corresponding detected macrodomains and CIDs based on directional index method9. Stars show the significant borders detected in both Lioy et al. data8 and the present one (black), only in Lioy et al. data (red) and only with our data (green). b, Domains detected based on DI analysis only at different resolutions; 1 kb (cyan), 2 kb (green) and 5 kb (blue). c, Bundle domains called using insulation score detection at 1 kb (cyan), or DI analysis on contact maps binned either 2 kb (green) and 5 kb (blue). Top, visualization of domains over the entire genome. Middle, magnification of a 500 kb region. Below, Corresponding RNA-seq track in CPM. d, Violin plot distributions of transcript levels for all genes in the genome (black), and for all genes in 10 kb windows centered on the domain boundaries called on the 5 kb (blue), 2 kb (green) and 1 kb (cyan) binned maps. The bars represent the first and ninth deciles, and the dots is the mean of each distribution. The p-values of non-parametric one-sided Mann-Withneyu test of whether the later distributions follow a genomewide distribution are indicated. e, Gene transcription in RPKM depending on the distance from the closest borders detected at different resolutions. The errors bars are defined as the 95% confidence interval of 1,000 bootstraps.
