Fig. 1

Gene-specific alterations in DNA methylation in DS frontal cortex neuronal and glial cells, cerebellar folial cortex, and T lymphocytes. a, b Supervised hierarchical clustering of the 450K methylation BeadChip data (fractional methylation values; AVG_Beta) for probes that passed ANOVA at p ≤ 0.001 and absolute difference in methylation ≥ 0.15 in DS versus control adult whole frontal cortex, glia, and neurons. Biological samples are on the x-axis and differentially methylated loci are on the y-axis, with relative hypermethylation and hypomethylation indicated by the color scale. For generating the heatmaps, the fractional methylation values for each CpG were renormalized using the default settings in dChip to have mean 0 and standard deviation 1. The red color represents a methylation level above the mean methylation of the CpG across all samples, the white color represents mean methylation and the blue color represents methylation lower than the mean. c Venn diagram emphasizing that many of the DS-DM genes are unique to either neurons or glia, with smaller sets of pan-cell-type DS-DM loci. d Partial lists of DS-DM genes, highlighting examples with relevant biological functions. The complete lists of DS-DM CpGs and genes are in Tables S3–S7 in Additional file 2. STDEV standard deviation