Fig. 4

A screenshot of the results of CMAcorrel for analysis of 5746 CpG loci with correlation coefficients higher then 0.18 (and r < − 0.18) between the levels of DNA methylation and gene expression. We analysed 500 bp regions around each CpG. At the right there is the composite model consisting of two composite modules with 10 PWMs each. At the left there is the plot of DNA-methylation-gene expression correlation versus the composite score of the region around CpG. Spearman correlation coefficient = 0.38. PWMs are the Position Weight Matrices (PWMs) selected by CMAcorrel algorithm to be included into the model consisting of two composite modules. Below each matrix name are the cut-off values given that were optimized by the CMAcorrel algorithm (in cases of cut-off = 0.0 the original profile cut-off was chosen by the algorithm). The parameter N (e.g. N = 2) gives the number of top scoring TF sites in the sequence that were considered for score calculation. The module width is the sigma value of the score (see Methods section)