Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization
Figure 5
Overlay Plots of Significant Regions of Wavelet Scalograms for Various E. coli Parameters
(A) Degree of significant pattern overlap in expression, gene density, and codon adaptation in E. coli. Binary matrices corresponding to significant regions of wavelet scalograms (FDR < 5%) for gene expression, CAI, and fractional gene density in E. coli were summed as described in Materials and Methods. A periodic pattern of 600–650 kb can be seen across nearly three-quarters of the chromosome.
(B) Degree of significant pattern overlap sequence-derived DNA-bending parameters in E. coli. Binary matrices corresponding to significant regions of wavelet scalograms (FDR < 5%) for intrinsic curvature, DNAseI sensitivity, protein-induced deformability, propeller twist, stacking energy, and nucleosome position preference in E. coli [12] were summed as described in the text. The white contour lines outline the significant regions of the wavelet scalogram for GC/AT content, thus demonstrating that these parameters are not independent.