Fig. 2

Differential expression and correlations between the levels of tRNA p9 methylation and nuclear gene expression in BRCA. a Volcano plot of statistical significance (shown as the negative logarithm of the P value on the y-axis) versus magnitude of differential gene expression (shown as the log base 2 of magnitude of mean expression difference on the x-axis) of 99 genes encoding mtRNA-binding proteins. The dashed line indicates Bonferroni statistical significance. b Distribution of Spearman correlations between gene expression levels of the 99 genes and the levels of methylation at p9 site 10413. Associations that are significant at Bonferroni threshold in normal samples are highlighted with the dark green color. c Two-way clustering of Spearman correlations of expression levels of 16,736 genes (columns) and methylation level at 11 p9 sites (rows) in the BRCA dataset. Correlation values are visualized using a red-to-gray-to-blue color theme (values range from 0.62 to −0.66). d Ingenuity pathway enrichment analysis of nuclear genes whose expression levels are associated with the levels of methylation at p9 site 10413 in the BRCA dataset. The top four categories are shown and the P value represents the most significant biological sub-function within each category