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Figure 4 | Genome Biology

Figure 4

From: Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma

Figure 4

Correlation of HOXA10 expression and DNA methylation at the canonical and alternative promoter in 59 NCH_EORTC samples, stratified by CHR7 status. The genomic organization of the HOXA10 region on CHR7 is illustrated in (A) based on RefSeq annotation, retrieved from Ensembl using reference genome hg19/GRCh37. In addition the location of Infinium 450k probes are shown by grey bars at the bottom of the panel. Red bars highlight the location of the CpGs used for the plots in (B) and (C). In (B) four X/Y plots show the correlation between DNA methylation of two CpGs located in the canonical HOXA10 promoter (Region 1) and expression of the Affymetrix probe 214651_s_at. The top row of panels (B) and (C) show the expression and DNA methylation of samples with gain of CHR7 (n = 38). Bottom row of panels (B) and (C) show the corresponding data from samples with normal CHR7 status (n = 21). The CHR7 status was given by normal mixture model based on the weighted mean of the segmented copy number. Pearson’s product moment correlation coefficient (cor) and P values are shown above each plot. Black lines in the plots show the fit of linear regression, in green local regression using lowess smoothing is shown. Figure S10 in Additional file 1 shows the correlation between gene expression and DNA methylation for 103 TCGA samples.

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