Fig. 6: Correlation between differential methylation in newborn dried bloodspots and differential gene expression in fetal liver CD34+ cells in Down syndrome (DS) and non-DS samples.
From: The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis
a Volcano plot showing differential gene expression between DS (N = 3) and non-DS (N = 3) FL CD34+ cells, with significantly upregulated and downregulated genes (FDR-adjusted P < 0.1) highlighted in red (N = 294) and blue (N = 293), respectively. b Bar chart showing the number of hypomethylated (N = 372) and hypermethylated (N = 357) DS-associated differentially methylated regions (DMRs) that overlapped gene promoters/enhancers, and the direction of differential expression of the corresponding genes in DS versus non-DS FL CD34+ cells. For hypomethylated DMRs, 96 genes were downregulated and 167 genes upregulated (109 genes not expressed), whereas for hypermethylated DMRs, 134 genes were downregulated and 94 genes upregulated (129 not expressed), a difference that was highly significant in a two-sided Fisher’s exact test (P = 9.20 × 10−7). c DS-associated DMR methylation levels and corresponding differential gene expression levels across chromosome 21. The zoomed-in plot below highlights four genes that play an important role in hematopoiesis, RUNX1, DYRK1A, ERG, and ETS2, all of which were overlapped by hypermethylated DMRs in promoters/enhancers and also demonstrated less than the expected 1.5-fold change in expression (indicated by the red horizontal line) in DS compared to normal FL CD34+ cells.
