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Figure 1 | Genome Biology

Figure 1

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 1

Cross-correlation of HOX-signature gene expression and DNA methylation of top 100 associated CpGs. (A) The heatmap visualizes the correlation between top 100 450k probes measuring DNA methylation of CpGs located in CpG islands of the HOXD, PROMININ1, HOXA, and HOXC loci (x-axis, see Additional file 1: Table S1 for detailed probe information) and the expression of 21 HOX-signature genes measured by 22 Affymetrix HG-133Plus2.0 probes (y-axis) in the NCH_EORTC GBM cohort. The probes on both axes are ordered according to chromosomal location. The chromosomal locations of the HOX-signature genes are color-coded. (B) Mean correlation between each selected CpG and expression of the HOX-signature genes of the NCH_EORTC dataset in A. The plot in (C) displays the mean correlation of the validation set comprising 106 GBM samples from TCGA using the same set of Infinium 450k probes and a total of 53 Agilent probes measuring expression of HOX-signature genes (see Additional file 1: Figure S3 for the corresponding heatmap). Circles highlight probes, which showed a statistically significant mean correlation between DNA methylation at measured CpG probes and the probes measuring expression of HOX-signature genes (q-values, FDR < =0.1). See also Additional file 2: Table S2 for list of Illumina Infinium 450k probes.

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