Table 1.
Number of DMR.
Figure 1.
Validation of microarray results using MALDI-TOF mass spectrometry (MassARRAY).
CtDMRs are labeled by the gene symbol of the closest gene. Each ctDMR is shown as a heatmap; methylation level for each informative CpG fragment is shown in columns and analyzed samples are organized in rows. Each colored rectangle corresponds to 1 CpG unit. All three genotypes were analyzed. White spaces are shown when the quality of data was not sufficient to assess methylation. A) ctDMRs which are methylated in HMF according to microarray. B) ctDMRs which are methylated in HMEC according to microarray. A more detailed view for each analyzed region is included in Information S1.
Figure 2.
A) Position of ctDMR relative to TSS. Negative and positive distances correspond to sequences upstream and downstream to TSS, respectively. B) Position of ctDMR relative to the nearest CpG island. For both charts, pink lines show the expected distribution if DMRs have random localization and uneven microarray coverage is taken into consideration. 99% confidence interval based on the simulation is shown.
Figure 3.
Average histone modifications in post-stasis post-selection HMEC in regions proximal to ctDMRs.
For each group of ctDMRs, the signal enrichment from ChIP-Seq experiment performed on post-stasis HMEC was analyzed [35], [36]. All data points were grouped and a moving average along the distance from each ctDMR is shown. The microarray average was calculated from the same number of regions as ctDMR but randomly placed in the genome according the array coverage. Control profile is derived from input DNA signal of a chip-seq experiment. M+ = hypermethylation; M- = hypomethylation.
Figure 4.
Comparison of ctDMRs with breast cancer specific DMRs.
Number of unique and common DMRs is shown in Venn diagrams. Data for breast cancer specific DMR were reported previously [23]. Numbers in Venn diagrams show the number of regions; number of probes on the microarrays which are covering these region are show as numbers in parenthesis. Histograms below Venn diagrams show expected number of overlapping regions if positions of DMRs are random. Histogram is based on 5000 iterations of simulation. Red line shows the observed number of overlapping DMR.
Figure 5.
Comparison of methylation status in ctDMRs in HMF (Fb), HMEC and cancer cell lines (CCL)
Methylation status of CpG sites 87 ctDMRs was analyzed by MassARRAY. Individual CpG and sample types were ordered by hierarchical clustering. Within heatmap, red and green correspond to hypermethylation and hypomethylation respectively.