Fig. 1

Example of how some gene regions were chosen for examination in this study on the basis of available RRBS DNA methylation profiles for breast cancer cell lines and normal cell cultures and tissues visualized in the UCSC Genome Browser [13]. a The EN1 gene structure with exons as heavy horizontal bars; b, the aligned CpG islands in the illustrated region.; c, DNA methylation (ENCODE/RRBS/HudsonAlpha) profiles for the indicated cell cultures and normal tissues using an 11-color, semi-continuous scale (see color key) to indicate the average DNA methylation levels at each monitored CpG site; d, aligned transcription results indicating that the non-transformed breast cancer cell line is not transcribing this gene irrespective of its lack of DNA methylation. Paradoxically, normal myoblasts are transcribing it despite some upstream DNA methylation. All data are from ENCODE [19]