Fig. 2

Assessment of measurement bias and cell-type specificity present in half-life data. a PCA of all human samples except those from an outlier study [46], with sample names colored according to cell type and corresponding data point colored according to measurement approach. Axes are labeled according to the percentage of variance among samples explained by the first two PCs. See also Additional file 1: Fig. S3 for the same analysis using all samples. b Boxplot of sample distributions along PC2, partitioned according to the measurement method (i.e. pulse labeling or transcriptional shutoff). Replicates for the same study were first averaged according to their PC2 value prior to assessing differences between the methods, with statistical differences between distributions evaluated using a two-sided Wilcoxon rank-sum test. c Evaluation of the Pearson correlations between pairs of half-life samples. Considered in this plot were the subset of pairs of two different studies that interrogated half-lives in either the same cell type or different cell types. Statistical differences between the distributions were evaluated using a one-sided Wilcoxon rank-sum test to assess whether correlations from the same cell type exceeded those from a different cell type. d, e These panels are the same as those in a and c, respectively, except compare mouse samples. f Comparison of consensus, cell-type agnostic (i.e., methodology and cell-type independent) measurements of human and mouse half-lives among one-to-one orthologous genes. Half-lives for each species were computed as PC1 of the respective gene × sample matrix. Also indicated are the Pearson (r) and Spearman (rho) correlation values as well as sample size (n) of genes considered. Shown in all boxplots are the median value (bar), 25th and 75th percentiles (box), and 1.5 times the interquartile range (whiskers)