Comparison of expression quantification methods. (a) Heatmap of correlations between PolyA+ experiments from various cell lines and cell compartments. Experiments from the same expression quantification methods tend to cluster together, and CAGE and RNA-PET are closer to each other than they are to RNA-Seq. The clustering tree also shows that experiments on different cell compartments in the same cell line tend to group together and RNA expression from the cytosol (blue) and whole cell (black) tend to group together rather than with that of the nucleus (light blue). Code for cell lines: K, K562; G, GM12878; 1, H1-hESC; H, HepG2; E, HeLa-S3; N, NHEK; U, HUVEC. (b) Boxplot of correlation coefficients for all expression prediction in CAGE, RNA-PET, and RNA-Seq categories. Paired Wilcoxon test shows that CAGE-based expression data are significantly better predicted than RNA-Seq-based expression data (P-value = 3 × 10-5).