Fig. 3

Relationship among methylation, gene expression and TFs. A Volcano plot representing the differentially expressed genes (adj. p ≤ 0.05, red) associated with the differentiation of MSCs to osteoblasts. B Lowess curve representing the correlation between the expression of genes in arbitrary units that had CpGs differently methylated in their 5’UTR and the methylation of these CpGs (M values). C Association of Hypo- and Hyper methylated CpGs to the chromatin interactions mediated by the RNA polymerase II (POL II). Data from chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) was obtained from ENCODE repository. Bars represent the number of CpGs that overlap (or not) to the POL II-mediated interactions. The methylation of CpGs overlapping or not POL II regions is significantly different p = 0.0436 (Fisher’s exact test). D Output of the REINS algorithm that overlaps hypo- of hypermethylated CpGs and TFs to suggest potential activity. Bars represent the metric RRT (Relative Relevance of a TF). RRT is the ratio of the percentage enrichment in hypomethylated CpGs vs the percentage enrichment in hypermethylated CpGs for a given TF. Bars represent the log2 of the RRT for all the TF studied