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Fig. 5 | Genome Medicine

Fig. 5

From: Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies

Fig. 5

Correlation of chromosome arm-wide methylation levels and chromosome arm-wide gene expression. a For each tissue with available normal methylation data, we plot the mean arm-wide methylation levels of each arm (left column) and the mean arm-wide expression levels of each arm (right column). The mean expression and methylation values are quantile normalized to the same scale (see the “Methods” section) for comparison and visualization. For left column: the redder the color, the higher the arm-wide methylation level; the bluer the color, the lower the arm-wide methylation level. For right column: the redder the color, the higher the arm-wide expression level; the bluer the color, the lower the arm-wide expression levels. Bar plots besides the heatmap are Spearman rank correlations (horizontal bars indicate comparison for each arm independently; vertical bars indicate comparison for each tissue independently). The size of bubbles indicates the p value. A size of 2 indicates p value < 0.01, a size of 1 indicates p value < 0.1, and size of 0 indicates p values < 1. As seen at the tissue level, correlation between arm-wide methylation levels and expression levels is consistently negative (empirical p value after random shuffling the data < 0.05). b Leave One Out Cross-Validation Accuracy of predicting each tissue entity based on chromosome wide mean methylation levels of each sample. The height of the bar indicates the accuracy quantified as fraction of samples correctly classified. The numbers on top of each bar indicate the number of samples from a given tissue. c tSNE plot depicting the clustering of different tissue samples by chromosome arm-wide mean methylation levels

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