Fig. 1

Identification of potential tumor suppressor genes that are repressed early in LSC. a Heatmaps showing down-regulated genes (upper panel) and hypermethylated genes (lower panel) in LSCs versus HSCs, from GEO: GSE63270 and GEO: GSE63409, respectively. Log2 fold changes of gene expression (log2 FC expression, upper panel) and β-value differences in DNA methylation (meth_diff, lower panel) are displayed as bar graphs on the right. The heatmaps only represent the 34 genes that are simultaneously down-regulated and hypermethylated in LSCs versus HSCs. For LSC, n = 20 represents 20 LSC fractions from 10 patients. b Venn diagram showing the overlap of three gene sets including: 443 down-regulated genes (FDR < 0.05, log2 FC > 2) in LSCs versus HSCs, 535 hypermethylated genes (FDR < 0.05, methylation difference > 20%) in LSCs versus HSCs, and 1217 TSGs from the tumor suppressor gene database. The overlapping region (6) represents the finally screened tumor suppressor genes. c Boxplots showing gene expression (upper panel) and DNA methylation (lower panel) changes of PCDH17 in LSCs versus HSCs, from GEO: GSE63270 and GEO: GSE63409, respectively. The P values calculated with a Wilcoxon rank-sum test are shown