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Figure 3 | Genome Biology

Figure 3

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 3

HOX-signature expression levels are partially explained by DNA methylation and chr7p15.2 CNA. The linear model in (A) visualizes the relationship between DNA methylation of the probe cg05092861 (M-values) and CNA at the cytoband chr7p15.2 (log2 fold-change (FC) over normal reference sample), and its association with mean HOX-signature expression levels of the 59 NCH_EORTC GBM samples. The projected plane represents the predicted response, and illustrates that mean HOX-signature levels are highest for samples, which have an increase in CNA and decrease in DNA methylation. As additional information, the copy number status calls (based on segmented information from BAC CGH data) of all samples are illustrated by circles (normal CHR7) and triangles (CHR7 gain). See Additional file 1: Figures S7 and S8 for the HOX signature based classification of samples into HOX-high and -low. Analogue to the model used for the NCH_EORTC data, (B) illustrates the linear model for the 103 TCGA GBM showing the combinatorial effect of CNA increase and DNA methylation decrease on the increase of mean HOX-signature expression levels. CHR7 copy number status of individual samples is illustrated by circles (normal) and triangles (gain). Additional file 1: Figure S11 illustrates the organization of TCGA samples into HOX-high and -low groups.

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